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- PDB-7pmz: Crystal structure of Streptomyces coelicolor guaB (IMP dehydrogen... -

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基本情報

登録情報
データベース: PDB / ID: 7pmz
タイトルCrystal structure of Streptomyces coelicolor guaB (IMP dehydrogenase) bound to ATP and ppGpp at 2.0 A resolution
要素Inosine-5'-monophosphate dehydrogenase
キーワードOXIDOREDUCTASE / IMP dehydrogenase / guaB / BIOSYNTHETIC PROTEIN / EC.1.1.1.205
機能・相同性
機能・相同性情報


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / GTP biosynthetic process / ATP binding / metal ion binding
類似検索 - 分子機能
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain ...Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / IMP dehydrogenase / GMP reductase domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
ADENOSINE-5'-TRIPHOSPHATE / GUANOSINE-5',3'-TETRAPHOSPHATE / Inosine-5'-monophosphate dehydrogenase
類似検索 - 構成要素
生物種Streptomyces coelicolor A3
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.03 Å
データ登録者Fernandez-Justel, D. / Revuelta, J.L. / Buey, R.M.
資金援助 スペイン, 1件
組織認可番号国
Spanish Ministry of Science, Innovation, and UniversitiesPID2019-109671GB-I00 スペイン
引用ジャーナル: Protein Sci. / 年: 2022
タイトル: Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.
著者: Fernandez-Justel, D. / Marcos-Alcalde, I. / Abascal, F. / Vidana, N. / Gomez-Puertas, P. / Jimenez, A. / Revuelta, J.L. / Buey, R.M.
履歴
登録2021年9月4日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02022年5月11日Provider: repository / タイプ: Initial release
改定 1.12024年1月31日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
C: Inosine-5'-monophosphate dehydrogenase
D: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
H: Inosine-5'-monophosphate dehydrogenase
I: Inosine-5'-monophosphate dehydrogenase
J: Inosine-5'-monophosphate dehydrogenase
K: Inosine-5'-monophosphate dehydrogenase
L: Inosine-5'-monophosphate dehydrogenase
M: Inosine-5'-monophosphate dehydrogenase
N: Inosine-5'-monophosphate dehydrogenase
O: Inosine-5'-monophosphate dehydrogenase
P: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)863,63280
ポリマ－845,08916
非ポリマー18,54364
水64,0433555
1
A: Inosine-5'-monophosphate dehydrogenase
B: Inosine-5'-monophosphate dehydrogenase
E: Inosine-5'-monophosphate dehydrogenase
F: Inosine-5'-monophosphate dehydrogenase
G: Inosine-5'-monophosphate dehydrogenase
J: Inosine-5'-monophosphate dehydrogenase
L: Inosine-5'-monophosphate dehydrogenase
N: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)431,81640
ポリマ－422,5448
非ポリマー9,27232
水1448
タイプ名称対称操作数
identity operation1_555x,y,z1
2
H: Inosine-5'-monophosphate dehydrogenase
M: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子

C: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子

D: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子

I: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子

K: Inosine-5'-monophosphate dehydrogenase
O: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子

P: Inosine-5'-monophosphate dehydrogenase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)431,81640
ポリマ－422,5448
非ポリマー9,27232
水1448
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_656x+1,y,z+11
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation2_746-x+2,y-1/2,-z+11
crystal symmetry operation2_745-x+2,y-1/2,-z1
単位格子
Length a, b, c (Å)119.294, 300.896, 123.093
Angle α, β, γ (deg.)90.000, 90.280, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 7 through 46 or (resid 47...
21(chain B and (resid 7 through 9 or (resid 10...
31(chain C and (resid 7 through 9 or (resid 10...
41(chain D and (resid 7 through 9 or (resid 10...
51(chain E and (resid 7 through 9 or (resid 10...
61(chain F and (resid 7 through 91 or (resid 92...
71(chain G and (resid 7 through 46 or (resid 47...
81(chain H and (resid 7 through 9 or (resid 10...
91(chain I and (resid 7 through 9 or (resid 10...
101(chain J and (resid 7 through 46 or (resid 47...
111(chain K and (resid 7 through 9 or (resid 10...
121(chain L and (resid 7 through 9 or (resid 10...
131(chain M and (resid 7 through 46 or (resid 47...
141(chain N and (resid 7 through 46 or (resid 47...
151(chain O and (resid 7 through 46 or (resid 47...
161(chain P and (resid 7 through 91 or (resid 92...

NCSドメイン領域:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYVALVAL(chain A and (resid 7 through 46 or (resid 47...AA7 - 4610 - 49
12ARGARGARGARG(chain A and (resid 7 through 46 or (resid 47...AA4750
13GLYGLYALAALA(chain A and (resid 7 through 46 or (resid 47...AA7 - 47810 - 481
14GLYGLYALAALA(chain A and (resid 7 through 46 or (resid 47...AA7 - 47810 - 481
15GLYGLYALAALA(chain A and (resid 7 through 46 or (resid 47...AA7 - 47810 - 481
16GLYGLYALAALA(chain A and (resid 7 through 46 or (resid 47...AA7 - 47810 - 481
21GLYGLYPROPRO(chain B and (resid 7 through 9 or (resid 10...BB7 - 910 - 12
22GLUGLUGLUGLU(chain B and (resid 7 through 9 or (resid 10...BB1013
23GLYGLYLEULEU(chain B and (resid 7 through 9 or (resid 10...BB7 - 48010 - 483
24GLYGLYLEULEU(chain B and (resid 7 through 9 or (resid 10...BB7 - 48010 - 483
25GLYGLYLEULEU(chain B and (resid 7 through 9 or (resid 10...BB7 - 48010 - 483
26GLYGLYLEULEU(chain B and (resid 7 through 9 or (resid 10...BB7 - 48010 - 483
31GLYGLYPROPRO(chain C and (resid 7 through 9 or (resid 10...CC7 - 910 - 12
32GLUGLUGLUGLU(chain C and (resid 7 through 9 or (resid 10...CC1013
33GLYGLYALAALA(chain C and (resid 7 through 9 or (resid 10...CC7 - 47810 - 481
34GLYGLYALAALA(chain C and (resid 7 through 9 or (resid 10...CC7 - 47810 - 481
35GLYGLYALAALA(chain C and (resid 7 through 9 or (resid 10...CC7 - 47810 - 481
36GLYGLYALAALA(chain C and (resid 7 through 9 or (resid 10...CC7 - 47810 - 481
41GLYGLYPROPRO(chain D and (resid 7 through 9 or (resid 10...DD7 - 910 - 12
42GLUGLUGLUGLU(chain D and (resid 7 through 9 or (resid 10...DD1013
43GLYGLYALAALA(chain D and (resid 7 through 9 or (resid 10...DD7 - 47810 - 481
44GLYGLYALAALA(chain D and (resid 7 through 9 or (resid 10...DD7 - 47810 - 481
45GLYGLYALAALA(chain D and (resid 7 through 9 or (resid 10...DD7 - 47810 - 481
46GLYGLYALAALA(chain D and (resid 7 through 9 or (resid 10...DD7 - 47810 - 481
51GLYGLYPROPRO(chain E and (resid 7 through 9 or (resid 10...EE7 - 910 - 12
52GLUGLUGLUGLU(chain E and (resid 7 through 9 or (resid 10...EE1013
53GLYGLYALAALA(chain E and (resid 7 through 9 or (resid 10...EE7 - 47810 - 481
61GLYGLYVALVAL(chain F and (resid 7 through 91 or (resid 92...FF7 - 9110 - 94
62ASPASPASPASP(chain F and (resid 7 through 91 or (resid 92...FF9295
63GLYGLYALAALA(chain F and (resid 7 through 91 or (resid 92...FF7 - 47810 - 481
71GLYGLYVALVAL(chain G and (resid 7 through 46 or (resid 47...GG7 - 4610 - 49
72ARGARGARGARG(chain G and (resid 7 through 46 or (resid 47...GG4750
73GLYGLYALAALA(chain G and (resid 7 through 46 or (resid 47...GG7 - 47810 - 481
74GLYGLYALAALA(chain G and (resid 7 through 46 or (resid 47...GG7 - 47810 - 481
75GLYGLYALAALA(chain G and (resid 7 through 46 or (resid 47...GG7 - 47810 - 481
81GLYGLYPROPRO(chain H and (resid 7 through 9 or (resid 10...HH7 - 910 - 12
82GLUGLUGLUGLU(chain H and (resid 7 through 9 or (resid 10...HH1013
83GLYGLYALAALA(chain H and (resid 7 through 9 or (resid 10...HH7 - 47810 - 481
84GLYGLYALAALA(chain H and (resid 7 through 9 or (resid 10...HH7 - 47810 - 481
85GLYGLYALAALA(chain H and (resid 7 through 9 or (resid 10...HH7 - 47810 - 481
86GLYGLYALAALA(chain H and (resid 7 through 9 or (resid 10...HH7 - 47810 - 481
91GLYGLYPROPRO(chain I and (resid 7 through 9 or (resid 10...II7 - 910 - 12
92GLUGLUGLUGLU(chain I and (resid 7 through 9 or (resid 10...II1013
93GLYGLYALAALA(chain I and (resid 7 through 9 or (resid 10...II7 - 47810 - 481
94GLYGLYALAALA(chain I and (resid 7 through 9 or (resid 10...II7 - 47810 - 481
95GLYGLYALAALA(chain I and (resid 7 through 9 or (resid 10...II7 - 47810 - 481
101GLYGLYVALVAL(chain J and (resid 7 through 46 or (resid 47...JJ7 - 4610 - 49
102ARGARGARGARG(chain J and (resid 7 through 46 or (resid 47...JJ4750
103GLYGLYALAALA(chain J and (resid 7 through 46 or (resid 47...JJ7 - 47810 - 481
104GLYGLYALAALA(chain J and (resid 7 through 46 or (resid 47...JJ7 - 47810 - 481
105GLYGLYALAALA(chain J and (resid 7 through 46 or (resid 47...JJ7 - 47810 - 481
111GLYGLYPROPRO(chain K and (resid 7 through 9 or (resid 10...KK7 - 910 - 12
112GLUGLUGLUGLU(chain K and (resid 7 through 9 or (resid 10...KK1013
113GLYGLYALAALA(chain K and (resid 7 through 9 or (resid 10...KK7 - 47810 - 481
114GLYGLYALAALA(chain K and (resid 7 through 9 or (resid 10...KK7 - 47810 - 481
115GLYGLYALAALA(chain K and (resid 7 through 9 or (resid 10...KK7 - 47810 - 481
116GLYGLYALAALA(chain K and (resid 7 through 9 or (resid 10...KK7 - 47810 - 481
121GLYGLYPROPRO(chain L and (resid 7 through 9 or (resid 10...LL7 - 910 - 12
122GLUGLUGLUGLU(chain L and (resid 7 through 9 or (resid 10...LL1013
123GLYGLYALAALA(chain L and (resid 7 through 9 or (resid 10...LL7 - 47810 - 481
131GLYGLYVALVAL(chain M and (resid 7 through 46 or (resid 47...MM7 - 4610 - 49
132ARGARGARGARG(chain M and (resid 7 through 46 or (resid 47...MM4750
133GLYGLYALAALA(chain M and (resid 7 through 46 or (resid 47...MM7 - 47810 - 481
134GLYGLYALAALA(chain M and (resid 7 through 46 or (resid 47...MM7 - 47810 - 481
135GLYGLYALAALA(chain M and (resid 7 through 46 or (resid 47...MM7 - 47810 - 481
136GLYGLYALAALA(chain M and (resid 7 through 46 or (resid 47...MM7 - 47810 - 481
141GLYGLYVALVAL(chain N and (resid 7 through 46 or (resid 47...NN7 - 4610 - 49
142ARGARGARGARG(chain N and (resid 7 through 46 or (resid 47...NN4750
143GLYGLYALAALA(chain N and (resid 7 through 46 or (resid 47...NN7 - 47810 - 481
144GLYGLYALAALA(chain N and (resid 7 through 46 or (resid 47...NN7 - 47810 - 481
145GLYGLYALAALA(chain N and (resid 7 through 46 or (resid 47...NN7 - 47810 - 481
146GLYGLYALAALA(chain N and (resid 7 through 46 or (resid 47...NN7 - 47810 - 481
151GLYGLYVALVAL(chain O and (resid 7 through 46 or (resid 47...OO7 - 4610 - 49
152ARGARGARGARG(chain O and (resid 7 through 46 or (resid 47...OO4750
153GLYGLYALAALA(chain O and (resid 7 through 46 or (resid 47...OO7 - 47810 - 481
154GLYGLYALAALA(chain O and (resid 7 through 46 or (resid 47...OO7 - 47810 - 481
155GLYGLYALAALA(chain O and (resid 7 through 46 or (resid 47...OO7 - 47810 - 481
156GLYGLYALAALA(chain O and (resid 7 through 46 or (resid 47...OO7 - 47810 - 481
161GLYGLYVALVAL(chain P and (resid 7 through 91 or (resid 92...PP7 - 9110 - 94
162ASPASPASPASP(chain P and (resid 7 through 91 or (resid 92...PP9295
163GLYGLYALAALA(chain P and (resid 7 through 91 or (resid 92...PP7 - 47810 - 481

NCS oper:
IDCodeMatrixベクター
1given(0.0112840657433, 0.125788690778, -0.991992880586), (0.125123073336, 0.984081079721, 0.126208736043), (0.992077056674, -0.125545345621, -0.00463463198064)59.5949509073, -7.70917243737, -62.4729572892
2given(-0.010717217774, -0.12409474097, 0.992212495641), (-0.131411715417, -0.98348861642, -0.124423078339), (0.99126994421, -0.131721815337, -0.00576724110473)9.59009723477, -138.075658737, -1.21868687096
3given(-0.99994896548, 0.0100871680237, -0.000561673650949), (-0.0100884023449, -0.999946602045, 0.0022399101341), (-0.000539049308844, 0.00224546221113, 0.999997333659)70.1554761627, -145.684756253, -61.3493037003
4given(-0.972575848471, 0.232331900344, 0.0108677068624), (0.232209160476, 0.972598309752, -0.0114644519678), (-0.0132334712373, -0.00862646801306, -0.99987522186)120.193740178, -14.5988364013, -2.67975470331
5given(-0.41704254915, -0.0818614845461, 0.90519291289), (-0.0558840166291, -0.991741703072, -0.115435571096), (0.907167288257, -0.0987273606289, 0.409023739384)78.9714177306, -65.3571420978, -55.7124434388
6given(0.0291156363003, 0.129842570154, 0.991107051079), (0.112573492041, 0.984793363218, -0.132322487323), (-0.993216737984, 0.115425035142, 0.0140560538566)61.7291274078, -7.48582441249, 59.1140588161
7given(0.974253610133, -0.225228239234, -0.0101066015211), (-0.225097035072, -0.974254112214, 0.0126589745078), (-0.0126975566314, -0.0100580855778, -0.999868794878)68.5168493095, -132.006243576, 58.7493342006
8given(-0.0275695531833, -0.116401601554, -0.992819513755), (-0.111867778277, -0.986598812555, 0.118778715468), (-0.993340586063, 0.114339189347, 0.0141784998796)127.865124732, -138.778426712, -2.49436841982
9given(-0.914542871366, -0.013562923507, -0.404261528641), (-0.00632369636807, -0.998836112438, 0.0478166430728), (-0.404439547148, 0.0462867972153, 0.913392678483)108.141842281, -68.7466560999, 24.6754604438
10given(0.387923237113, -0.157202864788, -0.908186556501), (0.150041704332, 0.982974508852, -0.106059426303), (0.909397079976, -0.0951229428109, 0.404905639232)77.8311640303, 63.9128687367, 8.52124797952
11given(0.387205900488, -0.164513004636, -0.907197366582), (-0.151201812618, -0.981961146175, 0.113535541853), (-0.909510639019, 0.0932082545086, -0.405095814349)28.1260840428, -59.4303491861, 52.8155338724
12given(0.419214518041, 0.0798366512448, -0.904370110619), (0.0563707941545, 0.991915172692, 0.113695311026), (0.906135487347, -0.0986427863606, 0.411324785624)109.419140781, -80.890182686, 5.80170728164
13given(0.88939477348, -0.218787792606, 0.401383655265), (-0.223298327622, -0.974079008748, -0.0361654752094), (0.398891957538, -0.0574629143237, -0.91519572753)-0.370812476574, -55.5487804343, -27.6609174206
14given(-0.914616286824, -0.0120862909303, -0.404142263873), (0.00943636449519, 0.998642765009, -0.0512209226787), (0.404212818825, -0.0506611238179, -0.913260886949)157.629481947, 72.7137195692, 36.6272654532
15given(0.890879599158, -0.205187379392, 0.405255079107), (0.210002322648, 0.977140743105, 0.0330906731173), (-0.402781037645, 0.0556247022746, 0.913604579789)50.2277633658, 60.5991387965, -33.7770084617

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要素

#1: タンパク質
Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / IMPD / IMPDH


分子量: 52818.055 Da / 分子数: 16 / 由来タイプ: 組換発現
由来: (組換発現) Streptomyces coelicolor A3(2) (バクテリア)
遺伝子: guaB, SCO4770
発現宿主: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (大腸菌)
参照: UniProt: Q9L0I7, IMP dehydrogenase
#2: 化合物
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP


分子量: 507.181 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C10H16N5O13P3 / タイプ: SUBJECT OF INVESTIGATION / コメント: ATP, エネルギー貯蔵分子*YM
#3: 化合物
ChemComp-G4P / GUANOSINE-5',3'-TETRAPHOSPHATE / guanosine tetraphosphate;ppGpp / ppGpp


タイプ: RNA linking / 分子量: 603.160 Da / 分子数: 16 / 由来タイプ: 合成 / 式: C10H17N5O17P4 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物...
ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 32 / 由来タイプ: 合成 / 式: Mg / タイプ: SUBJECT OF INVESTIGATION
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 3555 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.63 Å3/Da / 溶媒含有率: 53.2 %
結晶化温度: 295 K / 手法: 蒸気拡散法, シッティングドロップ法
詳細: condition H9 of the commercial screening Morpheus-II: 0.01M Spermine tetrahydrochloride, 0.01M Spermidine trihydrochloride, 0.01M 1,4- Diaminobutane dihydrochloride, 0.01M DL- Ornithine ...詳細: condition H9 of the commercial screening Morpheus-II: 0.01M Spermine tetrahydrochloride, 0.01M Spermidine trihydrochloride, 0.01M 1,4- Diaminobutane dihydrochloride, 0.01M DL- Ornithine monohydrochloride, 15% w/v PEG 3000, 20% v/v 1, 2, 4- Butanetriol, 1% w/v NDSB 256 0.1M of the buffer system Gly-Gly, AMPD, pH 8.5

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: ALBA / ビームライン: XALOC / 波長: 0.999871222252 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2020年9月24日
放射プロトコル: SINGLE WAVELENGTH / 単色(M)・ラウエ(L): M / 散乱光タイプ: x-ray
放射波長波長: 0.999871222252 Å / 相対比: 1
反射解像度: 2.03→150.45 Å / Num. obs: 474239 / % possible obs: 94.2 % / 冗長度: 4.6 % / Biso Wilson estimate: 30.62 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.055 / Rrim(I) all: 0.11 / Net I/σ(I): 9.4
反射 シェル解像度: 2.03→2.15 Å / 冗長度: 4.5 % / Rmerge(I) obs: 0.991 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 23712 / CC1/2: 0.589 / Rpim(I) all: 0.528 / Rrim(I) all: 1.157 / % possible all: 58.1

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
autoPROCデータ削減
autoPROCデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 4AVF

4avf


解像度: 2.03→85.88 Å / SU ML: 0.21 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 22.67 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2125 23521 4.96 %
Rwork0.1798 450654 -
obs0.1814 474175 84.9 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 121.23 Å2 / Biso mean: 42.6357 Å2 / Biso min: 12.88 Å2
精密化ステップサイクル: final / 解像度: 2.03→85.88 Å
タンパク質核酸リガンド溶媒全体
原子数48287 0 1456 3569 53312
Biso mean--40.49 41.3 -
残基数----6842
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A28222X-RAY DIFFRACTION6.892TORSIONAL
12B28222X-RAY DIFFRACTION6.892TORSIONAL
13C28222X-RAY DIFFRACTION6.892TORSIONAL
14D28222X-RAY DIFFRACTION6.892TORSIONAL
15E28222X-RAY DIFFRACTION6.892TORSIONAL
16F28222X-RAY DIFFRACTION6.892TORSIONAL
17G28222X-RAY DIFFRACTION6.892TORSIONAL
18H28222X-RAY DIFFRACTION6.892TORSIONAL
19I28222X-RAY DIFFRACTION6.892TORSIONAL
110J28222X-RAY DIFFRACTION6.892TORSIONAL
111K28222X-RAY DIFFRACTION6.892TORSIONAL
112L28222X-RAY DIFFRACTION6.892TORSIONAL
113M28222X-RAY DIFFRACTION6.892TORSIONAL
114N28222X-RAY DIFFRACTION6.892TORSIONAL
115O28222X-RAY DIFFRACTION6.892TORSIONAL
116P28222X-RAY DIFFRACTION6.892TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.03-2.050.2718550.2641124112967
2.05-2.070.27921600.25822814297416
2.07-2.10.32352390.26084919515828
2.1-2.130.30673980.24977183758141
2.13-2.150.30124530.23749198965152
2.15-2.180.28215640.2378108861145062
2.18-2.210.28266350.2387127161335172
2.21-2.250.27027890.235145311532082
2.25-2.280.26168840.2272163331721793
2.28-2.320.26039070.2221171681807597
2.32-2.360.24899760.2137174611843799
2.36-2.40.25279810.2081756118542100
2.4-2.450.24928940.20841770818602100
2.45-2.50.24268810.20561765218533100
2.5-2.550.24128560.20431779118647100
2.55-2.610.24098680.19391770318571100
2.61-2.680.23179480.18031766218610100
2.68-2.750.23589200.1821765118571100
2.75-2.830.21269420.18221765218594100
2.83-2.920.22279870.18951764718634100
2.92-3.030.24158460.19431769318539100
3.03-3.150.2369520.18831777618728100
3.15-3.290.22529790.18221757418553100
3.29-3.470.20568430.17791774118584100
3.47-3.680.19648540.17351776418618100
3.68-3.970.19278620.15281782518687100
3.97-4.370.155710090.13491760318612100
4.37-50.165610240.13931759818622100
5-6.30.18779700.17221771918689100
6.3-85.880.20838450.18191788418729100
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6174-0.1531-0.09010.70110.31461.1877-0.06160.00650.08340.0392-0.0206-0.0244-0.0962-0.04610.05910.18010.01090.00370.15290.01730.191733.2663-56.383317.77
21.7342-1.64850.71121.2546-0.06150.1973-0.179-0.3760.15790.47350.1191-0.0443-0.0445-0.15220.05270.44770.08270.01770.3697-0.06020.296618.5229-35.900642.2056
32.247-0.53360.06462.5304-0.30832.8344-0.0742-0.3344-0.1810.42020.05490.42430.1656-0.3944-0.00420.30190.03090.08280.35180.01450.33136.2453-40.054837.9759
42.3599-1.53020.39642.81030.0350.9595-0.0585-0.28240.12120.290.0513-0.0853-0.0721-0.07550.00580.26820.01280.00810.1756-0.02330.17532.1797-55.927634.8244
52.446-0.5329-0.55410.91730.14621.69850.108-0.06870.07190.1112-0.0467-0.0357-0.10360.0302-0.05150.23670.00110.00360.20040.0210.213543.1071-63.997627.9697
62.91850.412-0.90821.6544-0.58873.36480.02810.24570.1314-0.08410.0310.106-0.1282-0.2202-0.09050.13130.02560.00550.14920.02060.139238.4091-65.756717.23
70.9871-0.8234-0.08051.78451.60311.82550.14770.16920.084-0.2507-0.1875-0.1161-0.29460.06370.09810.20440.0320.04160.180.01620.189635.2303-54.890914.0903
80.33760.6572-0.29361.7811-0.84760.42010.03370.09010.5578-0.1627-0.1931-0.4949-0.42460.21040.15060.53850.0273-0.03470.32660.05140.536136.4928-33.586819.9614
91.41740.06320.14320.80460.42482.17240.00690.0743-0.0257-0.0921-0.0250.04630.00360.02090.02650.21140.03960.01530.2334-0.00540.214829.8738-58.07366.6936
101.2303-0.4990.12110.51610.01071.12850.01620.0298-0.0053-0.072-0.0266-0.0114-0.0032-0.03590.01680.1387-0.01310.00670.1693-0.04020.175335.3255-57.1621-22.3542
110.91230.7333-0.57271.2495-1.27592.0273-0.11070.42410.6404-0.20180.38380.7089-0.2436-0.5252-0.23920.35530.0533-0.12280.47110.13430.585713.4592-35.4869-39.5167
121.56271.0816-0.15982.1621-1.23021.997-0.36020.76170.3124-0.78680.43380.52060.1597-0.3254-0.05840.4262-0.0456-0.16640.54860.06670.37618.5811-44.2203-47.1196
130.7276-0.245-0.28372.5408-1.89161.8198-0.09190.0485-0.00340.10670.07550.2004-0.2231-0.4817-0.00390.16280.030.00050.2453-0.01810.221215.9219-54.8367-18.5087
142.1731-0.10711.02491.27790.2663.1813-0.1556-0.02790.0138-0.0470.0110.1492-0.0644-0.13330.12210.150.01870.01620.155-0.03860.182824.3265-61.7043-11.6787
153.28120.04181.10741.95880.72813.741-0.050.0542-0.3186-0.22670.125-0.29790.03570.1579-0.01480.19110.01680.03380.2313-0.05130.23734.7636-65.4486-15.8264
161.648-1.935-0.08163.2469-0.98421.33160.01640.12120.13090.0443-0.3039-0.1442-0.11920.08240.21260.2143-0.0039-0.00980.2976-0.00630.210639.0813-55.7686-20.7326
171.70010.7860.0223.38610.43031.54620.328-0.45020.64650.4311-0.3619-0.0785-0.53920.3881-0.00490.5127-0.07080.01760.373-0.0690.429936.0137-33.7505-22.2351
182.3496-1.31290.01271.4371-0.832.4322-0.02760.0177-0.0396-0.0462-0.0276-0.14760.04960.21160.06710.1571-0.02210.01680.2443-0.02650.223846.0738-60.5326-25.21
190.9388-0.2485-0.15180.5912-0.02080.95610.06440.05080.0059-0.0711-0.06350.01560.05510.00890.01660.17650.00280.02480.19460.02570.177933.8037-88.856639.2008
201.55870.72970.0521.99840.77791.2844-0.11710.4452-0.3235-0.7090.2364-0.74390.03660.1692-0.13540.52150.06960.23180.409-0.04140.540855.1238-108.85917.5572
211.4025-0.3214-0.65541.80510.91961.6186-0.21160.2921-0.3595-0.83490.0638-0.6064-0.14160.15050.090.6285-0.00640.20470.4419-0.03620.440649.6882-101.963213.5461
220.82660.1050.30942.16411.60862.31770.01790.1523-0.0588-0.05160.0196-0.2075-0.02160.2954-0.02380.18990.03290.06720.22960.03590.24650.7948-91.626537.8944
231.3585-0.0945-0.532.31711.12571.9975-0.0025-0.0503-0-0.02840.0042-0.2794-0.0550.3197-0.06570.1732-0.00530.02810.23150.0530.204649.6512-81.564747.2951
241.8436-0.87941.09360.40430.43552.46310.12490.0132-0.04890.0048-0.0490.05340.2363-0.2059-0.09630.2449-0.00690.05710.2075-0.01480.240433.5204-84.859648.1086
251.3690.42610.38531.93790.39261.39370.2208-0.0314-0.41920.2541-0.3177-0.0430.448-0.32830.06150.4181-0.06710.03810.34110.02020.327233.6303-105.239339.5785
262.0272-1.0651-0.12681.28530.28762.1930.04890.11990.003-0.082-0.13560.1164-0.0488-0.10940.06430.1740.01090.0070.2585-0.00110.188423.3561-85.369635.9106
271.1697-0.31440.45210.7594-0.24961.5029-0.0566-0.0246-0.08140.0734-0.01050.05040.1446-0.02810.05950.2139-0.01410.05050.1383-0.02380.186736.1526-89.4253-43.7578
281.5477-1.81210.04693.1350.09510.2302-0.2173-0.2878-0.01590.66650.2178-0.21160.12040.0666-0.0020.4130.0182-0.03350.27140.00440.224248.2221-99.3695-23.6855
291.2487-0.8343-0.20880.4836-0.44850.99330.00430.1348-0.25540.0094-0.06250.12530.1486-0.16950.07720.2328-0.01870.03950.2173-0.03560.21928.9261-86.0692-44.3578
301.4952-0.4004-0.07081.3703-0.21461.2777-0.05220.0779-0.29530.0899-0.04250.04140.2699-0.03270.10680.28630.01760.05270.2251-0.05850.221737.5268-96.4107-50.192
311.60340.0558-0.20770.6489-0.24391.1554-0.0417-0.0024-0.19510.0698-0.0031-0.08620.01240.07140.04840.24330.05870.00730.2248-0.01210.263370.0063-68.3534-10.6615
321.95660.2931-0.28151.626-0.40591.97410.00090.2212-0.0631-0.0184-0.04710.0509-0.04350.00940.02020.19160.03810.03780.2938-0.03960.237679.0296-56.5537-28.9842
332.06251.6225-0.17021.6442-0.29780.477-0.12210.12290.2008-0.15710.13280.1229-0.0745-0.1872-0.0080.23790.052-0.00230.3212-0.00420.226189.5172-48.8041-43.6565
341.73110.02470.14541.83290.39022.2802-0.14840.22660.1946-0.43070.09690.1085-0.3394-0.07510.03680.30530.05350.00680.32240.02810.2423100.9243-40.8146-46.8527
351.99640.7178-0.06023.3120.68741.5395-0.01150.2859-0.0594-0.27950.0502-0.57690.23370.3037-0.04630.25980.06020.05790.3481-0.03360.2863108.7353-50.8202-42.1667
362.03570.8762-0.33681.1986-1.14871.02420.09580.0503-0.1113-0.0783-0.0074-0.0983-0.01990.1425-0.10580.16640.04540.03070.2369-0.01490.2088101.4832-54.2894-37.8939
372.24161.4652-0.55161.5809-0.30220.4375-0.07240.3822-0.0384-0.12540.02310.08750.0825-0.08160.04420.25540.03920.03070.39-0.05630.226476.0435-62.0385-37.3097
383.6757-0.207-0.3450.3465-0.47581.24830.00480.3084-0.1028-0.13260.0585-0.0830.0830.0858-0.04820.2353-0.00510.01530.26-0.05610.233863.6705-67.0939-30.4911
392.2383-0.3186-0.24611.5325-0.18793.0183-0.197-0.1195-0.13740.21170.265-0.35580.12650.1796-0.0320.21740.03770.01570.2493-0.04010.289967.6293-69.8009-19.8387
401.25260.8775-0.60461.3446-1.34631.45710.1584-0.14030.11650.1288-0.14720.3225-0.13190.0994-0.00450.15460.02480.04120.2369-0.03240.24873.3341-60.1627-16.7737
411.2001-0.67530.08852.81530.81841.5651-0.028-0.35590.6758-0.1619-0.07410.0852-0.4089-0.27730.08860.37540.0421-0.03240.3381-0.06710.489377.2185-39.0143-22.8261
422.13540.18310.07761.4204-1.1182.02140.0572-0.2167-0.11320.1064-0.0601-0.09810.00510.06420.00630.16590.02250.02640.2618-0.00660.208577.7976-64.3614-9.3421
431.3927-0.3492-0.41010.59960.30451.31550.07280.10830.0243-0.02760.0041-0.0380.08130.0217-0.05440.25220.0202-0.02290.1992-0.01150.244285.6833-13.2375-12.6907
440.853-1.4107-0.97211.98051.22650.8722-0.1396-0.1107-0.03180.21190.1234-0.1142-0.01750.04910.01920.24220.0627-0.0190.2554-0.03020.2976109.8474-31.6988-14.7966
452.12590.02620.96951.73390.03641.95010.13280.0087-0.44180.34180.1626-0.33430.20740.1275-0.2480.26210.06920.00140.2835-0.01780.3273115.7762-42.0589-22.5156
462.0241-0.5770.06982.53220.3122.0537-0.01660.32220.4387-0.2651-0.016-0.375-0.13840.19370.00040.2001-0.01130.06010.27840.02010.2995116.9952-33.0467-32.6383
472.332-0.9677-0.45632.21020.92262.4333-0.04940.08860.3062-0.1273-0.0034-0.2705-0.2839-0.0440.08880.26970.02260.00790.2538-0.00970.3664110.8711-27.7115-28.3656
481.094-0.7372-0.68332.34010.90751.92040.0173-0.04930.07130.13550.0077-0.27620.10660.28650.0050.26340.0488-0.05180.2657-0.0260.3647101.653-15.4716-6.852
492.4547-0.7416-0.90780.87040.27932.6094-0.0682-0.12390.06310.11060.0377-0.1103-0.07440.27690.00210.2429-0.0065-0.05260.2055-0.0080.286597.0738-4.80050.503
501.4832-0.5932-1.48080.4085-0.17783.2473-0.32160.2114-0.456-0.16820.08880.00540.5019-0.3310.15660.28290.0071-0.030.1973-0.03940.303881.9385-12.22362.1686
514.45140.5685-0.87171.1508-0.43122.5791-0.05960.4449-0.0224-0.18120.16110.04690.1554-0.2737-0.12470.25370.0244-0.0310.17270.01850.204483.5775-4.6201-7.2021
521.212-1.43010.16771.6146-0.00450.75510.11070.2543-0.28810.0523-0.16040.06160.0842-0.10210.02580.25760.0518-0.02210.2858-0.04190.277681.5451-14.3361-12.5722
531.96992.1933-0.17222.83050.60981.18260.1839-0.4317-0.41360.6825-0.2566-0.01880.5873-0.3528-0.09390.589-0.0839-0.02530.4026-0.02930.442685.0633-36.6838-11.1564
542.1398-1.07140.02071.17060.07281.96110.14440.2477-0.0522-0.2347-0.12850.1141-0.1151-0.0968-0.02970.24760.0486-0.03990.2614-0.0140.194377.4997-9.9475-20.1373
551.49-0.085-0.14180.54530.43631.55010.0087-0.0958-0.02640.0337-0.06710.0141-0.038-0.14570.07490.160.01490.01970.16820.05790.217562.4855-67.192215.8893
561.8204-0.2633-0.26181.9950.94052.2647-0.0119-0.28270.30110.13010.1354-0.4536-0.29430.6207-0.09020.2406-0.0781-0.04830.3778-0.00280.334789.7256-53.421628.0661
570.66850.1069-0.52630.15070.38391.49820.0792-0.170.4050.3030.7762-0.9112-0.49031.5754-0.30550.495-0.1971-0.23381.01-0.26310.7938101.7536-40.385243.6072
581.2791-0.368-0.12631.39440.59561.6568-0.268-0.3241-0.16450.92840.3011-0.39370.24460.7892-0.06630.69020.1115-0.18410.5856-0.01050.463492.5345-52.633349.2631
591.2133-0.1966-0.22361.93691.16821.36680.0034-0.12960.038-0.0180.1041-0.2639-0.05680.5153-0.06270.16150.0131-0.02480.31970.05940.29689.5761-63.661520.9041
600.96540.28380.38510.2214-0.27473.1258-0.04530.02220.02550.0545-0.0392-0.1792-0.01240.29920.05650.15930.03690.01630.23630.0390.256782.312-69.49559.2482
613.10750.49110.94781.131-0.56323.28020.1568-0.0124-0.20160.17010.15180.2504-0.07-0.1149-0.2760.22360.04790.00840.2390.05330.268771.3223-70.327813.2892
622.47832.36020.12132.58820.92791.10060.1473-0.30820.1939-0.221-0.350.1871-0.157-0.08780.21350.20.0446-0.00790.2286-0.00470.198769.6863-59.397117.9306
631.0655-0.1658-0.14211.5745-0.40221.07120.16290.13970.1321-0.4063-0.1478-0.1682-0.0093-0.17990.01410.51880.0067-0.00740.27170.00210.408478.242-39.148319.4018
642.20510.55470.41880.80750.32142.46930.0197-0.15480.03330.0969-0.03050.0711-0.0509-0.27350.00980.16920.03330.02310.21140.010.173261.8334-62.277222.8246
651.54690.36760.62540.22620.18360.8528-0.00260.06450.0921-0.0235-0.02830.01850.0148-0.00250.03230.17830.0550.01490.18420.01330.2027113.6481-84.206141.1488
661.65191.12630.4471.0560.06970.5587-0.0070.0721-0.2052-0.2291-0.0145-0.07340.10230.09160.01810.3050.0936-0.01450.2978-0.02870.277998.8416-97.553317.9262
671.42010.3252-0.2481.6946-0.32782.50450.07050.1538-0.2245-0.7017-0.1251-0.10350.72560.06930.03130.41970.0847-0.04280.2679-0.05020.27387.5724-105.63714.6863
682.30990.37670.44531.8917-0.98031.71270.13130.0573-0.0478-0.14940.04890.27330.0008-0.2235-0.21590.26480.0641-0.01440.27980.00750.279483.239-93.928121.3931
691.9221.32840.4291.6932-0.1010.7786-0.07850.51810.1247-0.18870.04770.0021-0.0510.06410.01920.22630.0545-0.00580.36770.04270.2068112.2732-84.16624.193
703.7858-0.22221.07280.53690.52211.09090.05790.26640.0533-0.15740.04460.084-0.07560.0258-0.0950.23560.02450.02560.24220.03110.1827124.7077-79.031330.9098
712.22350.81790.64060.40750.85381.47580.1166-0.08680.0041-0.06-0.16270.06840.0902-0.0550.03970.17490.04890.00940.21040.00690.2101118.1125-81.204543.074
721.39660.1069-0.22053.5539-0.95781.42240.0955-0.3922-0.6683-0.3075-0.4805-0.20150.53510.27370.34650.39960.06840.06150.38490.08710.4432111.4016-107.418338.5366
731.37140.43880.2191.16080.67032.03940.0278-0.17730.12720.0366-0.0350.1406-0.0774-0.02950.01350.21020.02290.01750.3119-0.02060.2429110.4402-81.814752.0634
740.87360.0268-0.22620.3545-0.24221.76190.0592-0.1165-0.02780.0163-0.04130.08040.0415-0.0851-0.01090.25020.00060.03390.2634-0.07830.2957115.9709-84.4427-41.907
750.08-0.13460.55411.9482-0.7811.7814-0.0731-0.2012-0.1260.61270.23390.79010.063-0.6362-0.10660.5117-0.09210.26670.69720.02350.637590.5543-98.6518-19.972
760.3088-0.71760.17821.8621-1.08691.5903-0.0334-0.207-0.0620.26820.09030.3679-0.0471-0.4090.00430.2911-0.0670.07960.4662-0.03810.4066100.2346-85.993-34.4744
771.2470.6854-0.1250.66950.14142.91910.00410.0057-0.02760.0649-0.07860.19990.0269-0.31650.04370.22760.02710.03160.3218-0.04990.3277106.5462-77.0732-52.3921
782.17880.1152-0.49410.73710.36882.390.1222-0.08970.01140.10780.0111-0.1260.05510.21-0.12180.21940.04280.0290.2874-0.05650.2743117.3396-76.432-48.3785
792.56931.9752-0.16952.0513-1.09861.33680.0791-0.33-0.14740.0482-0.28970.1360.26720.09490.15660.26740.03910.05710.2735-0.03130.2759119.2837-86.7151-43.5909
800.8069-0.7627-0.22552.54661.08121.1104-0.01880.2697-0.1891-0.4248-0.134-0.06920.19760.0329-0.18190.5061-0.02980.01430.342-0.0180.5363110.7264-106.8426-42.3456
811.80040.3689-0.11370.8183-0.47151.6181-0.0091-0.075-0.09590.1056-0.0007-0.0056-0.00710.10310.01010.22910.01360.0390.309-0.03040.249127.0355-83.8061-38.7506
820.71010.0365-0.17350.7961-0.23590.75960.0132-0.1342-0.05560.0651-0.0423-0.02030.04220.01640.00790.2445-0.0114-0.02670.2022-0.03190.207571.3919-11.629624.7529
831.4251-1.53740.65671.9661-0.31190.7408-0.2116-0.3281-0.14610.84060.2958-0.11920.0938-0.0396-0.11670.75980.0258-0.10790.49510.06550.325878.6859-30.464755.2459
840.7791-0.74880.93871.5808-0.99411.0202-0.0607-0.21790.13070.86960.1565-0.5040.124-0.0462-0.05950.69250.0234-0.23330.4312-0.00860.363585.7812-24.497951.4617
852.2769-1.47610.29692.6306-0.19060.7718-0.0474-0.44920.1010.37980.06020.1050.1001-0.0350.00940.3551-0.0224-0.01520.2971-0.03230.213665.4368-11.425940.8937
861.6346-1.00620.3222.8619-0.47431.3439-0.0157-0.3280.09020.3368-0.05110.2022-0.0867-0.10830.04860.2582-0.01870.01040.275-0.10680.252359.1855-0.621535.0075
872.61270.09910.05160.43-0.44361.20550.03610.0729-0.07720.0462-0.08220.04220.147-0.05250.00730.25290.0135-0.00960.2036-0.0480.256261.9196-5.735821.3355
881.47580.2353-0.60391.0242-1.17541.35830.1989-0.0315-0.153-0.1728-0.34310.1850.25850.04330.04980.28710.0134-0.04440.2226-0.04190.254570.9421-13.441320.6664
891.061-0.1094-0.37232.2311.20510.99140.09080.3374-0.7132-0.0514-0.29220.35930.4505-0.01910.11560.49020.0031-0.05250.2798-0.01870.53967.3575-34.516126.5007
901.7838-0.0372-0.18020.947-0.47481.57690.02750.05-0.0139-0.044-0.0694-0.110.11140.09260.03880.25560.0418-0.02030.2182-0.02810.245778.894-10.411715.9453
911.6099-0.15130.65630.2809-0.15330.97370.1167-0.0137-0.08520.0464-0.0155-0.05660.0374-0.0569-0.08840.2826-0.0076-0.02260.2169-0.0650.276783.651611.370951.5021
921.5118-0.54240.79981.7494-0.28081.1213-0.0145-0.22820.13750.1652-0.09010.3351-0.0628-0.16690.0940.23660.01280.03910.2948-0.06850.293255.933623.313749.3766
932.3520.5723-0.52852.3372-0.72232.6354-0.01660.06630.2456-0.032-0.01630.3242-0.0599-0.25850.0010.2150.0226-0.04250.2587-0.08160.387348.068427.399535.9612
941.7499-0.66471.46890.9237-0.60431.12940.1687-0.2718-0.23290.0744-0.01820.1380.1395-0.2348-0.13670.2431-0.0490.00620.2541-0.01750.273166.50589.546153.5633
951.4277-0.67780.77130.0997-0.74712.43440.1351-0.027-0.0110.0488-0.12590.0573-0.02730.0739-0.01770.3068-0.0202-0.02530.2371-0.0320.300587.4439.224258.1885
961.22650.84880.07653.58420.20111.5237-0.0766-0.11410.34310.3802-0.33470.2369-0.3490.17290.37890.529-0.04040.00980.3134-0.02210.395879.07434.133852.8027
972.5176-1.14860.00220.5729-0.26381.82020.20160.1428-0.1304-0.1212-0.13490.01130.14170.0825-0.08540.2340.02580.00350.2045-0.04510.274492.391510.286843.9245
982.01910.3151-0.58060.2982-0.14370.62240.04130.05320.1771-0.0137-0.01530.0294-0.0236-0.1125-0.01130.21740.0492-0.01860.1927-0.0260.255229.1935-8.318110.0112
992.1012-0.56970.40321.264-0.52022.3384-0.05720.1158-0.264-0.23810.00680.23440.2764-0.29510.0330.26940.0213-0.03270.3178-0.12010.3796-1.1901-26.345717.8951
1001.52610.6789-0.63683.0649-0.00231.666-0.2419-0.37340.26080.42260.08520.1456-0.2215-0.19220.12680.28670.1293-0.01950.3646-0.11840.34081.1772-15.263333.233
1012.0210.5462-0.73571.5618-0.04232.3646-0.0425-0.1754-0.0755-0.0289-0.12870.2003-0.2424-0.14040.15220.22950.0811-0.04810.2539-0.10510.28966.4253-14.943525.8443
1021.46890.5778-0.79981.6369-0.69191.2393-0.02440.22490.353-0.15170.00550.0957-0.0719-0.3791-0.01650.23330.0633-0.02550.31770.01250.333518.5882-5.25784.2379
1032.17860.4137-0.68260.1320.07892.24180.05340.23630.2623-0.07570.01460.1564-0.1805-0.2057-0.08750.29230.0791-0.02250.25270.04350.374532.23360.7293-2.2402
1042.81140.91640.49240.3546-0.48633.63860.23060.15620.0093-0.2184-0.1337-0.02710.19730.0564-0.0870.20410.0259-0.00260.1573-0.03030.274938.8016-4.06328.8623
1050.44250.2628-0.23932.6042-0.41131.04340.0605-0.126-0.2596-0.3685-0.2753-0.43170.42630.05290.15710.3990.05930.02660.30320.01840.370830.785-23.40938.6723
1062.62740.8046-0.15030.2761-0.17031.95090.0956-0.19490.12130.1015-0.05070.0174-0.06310.0942-0.0350.23280.0251-0.01870.1605-0.0360.24543.1685-6.107217.5131
1071.5876-0.56210.08340.4574-0.0731.17880.11090.0614-0.1165-0.0499-0.03360.0982-0.0708-0.0655-0.06820.2333-0.0268-0.03590.19080.03450.3047102.8554-133.108948.7231
1081.113-1.46761.11171.6254-1.04110.8798-0.1133-0.1394-0.14860.19490.16010.19640.0105-0.1579-0.0230.28870.04140.02180.30070.08570.417478.6815-114.627746.9508
1092.5506-0.619-0.56131.205-0.44612.09250.01410.0059-0.2681-0.06410.06580.32250.0415-0.2463-0.09520.26210.0195-0.05010.28230.03210.425173.8723-111.880934.0267
1100.5765-0.0807-0.29862.0608-0.76351.73460.04690.0422-0.05560.1019-0.06280.135-0.1083-0.26850.04190.23560.0438-0.00780.28190.07620.439187.1277-130.811454.7176
1111.6215-0.57330.83990.24640.10842.1104-0.12460.03140.0024-0.02030.11090.21220.0094-0.07380.00310.2478-0.0343-0.01340.21950.08170.384597.1119-138.778762.6362
1123.2714-0.31430.00911.1418-0.28192.4277-0.15010.0589-0.0948-0.20610.23520.1251-0.1310.1339-0.04830.2578-0.0288-0.03820.20390.02550.315105.0749-141.641354.2848
1130.17720.5667-0.23273.1144-0.82021.03380.1924-0.00740.18330.2616-0.2344-0.1276-0.32270.15330.01110.3283-0.0401-0.03750.31960.07350.4169105.348-120.879649.4867
1141.7506-1.05180.16560.8751-0.08821.62650.17170.0322-0.0701-0.2481-0.0723-0.01560.1610.1185-0.10920.29490.0043-0.05340.27250.05330.3046111.3177-136.197141.4046
1150.77610.33420.34470.74770.31081.0791-0.07280.2721-0.0266-0.22380.09790.0626-0.0362-0.151-0.02890.32570.0071-0.02630.42730.05060.277247.1734-13.6877-36.7696
1161.76090.6777-0.29641.6675-0.00750.9232-0.21360.43710.0828-0.67170.23380.1788-0.03130.0498-0.02240.5642-0.1228-0.12050.58750.06540.317131.1693-22.8628-58.5139
1171.53150.96160.70651.23930.49660.861-0.08930.3812-0.0773-0.22960.122-0.0050.00810.0812-0.01450.3311-0.0164-0.02230.47240.07650.258654.3547-9.5197-43.1416
1181.9508-0.15650.9990.9220.0732.4826-0.12050.29250.1221-0.18820.1529-0.0119-0.04570.02520.01980.27620.0016-0.00340.33440.07460.268963.1736-3.937-32.2871
1191.5670.005-0.19681.21670.52712.8542-0.05720.11480.19950.02740.11090.16290.0539-0.0877-0.06380.29590.0474-0.05060.40090.11170.367155.1574-1.0848-24.0744
1201.58110.78180.18250.99980.73440.8460.0795-0.1306-0.37580.1626-0.1715-0.21870.2572-0.16680.08490.3852-0.0049-0.03790.40260.08750.359348.0055-21.183-26.4613
1211.638-0.0295-0.06220.89191.4792.2644-0.01130.00220.2146-0.1203-0.03170.1053-0.0736-0.22180.03310.25680.0238-0.0290.30660.05640.270741.6237-5.4984-18.6662
1220.53670.2714-0.02341.0875-0.10551.06230.06650.19260.0887-0.34810.0303-0.0329-0.16410.0107-0.08340.40770.10070.02620.3463-0.04220.3266120.971420.762727.7236
1230.81461.04850.34182.15610.76590.8626-0.17790.2329-0.0547-1.20760.2169-0.2654-0.07960.1106-0.03541.01130.06930.26150.57380.0040.4302133.960533.93996.2209
1240.7330.66360.09752.08030.32761.07710.14050.34170.1207-0.2729-0.01960.1517-0.17360.0257-0.09160.40660.1152-0.00090.3579-0.06650.2727114.938615.337920.979
1252.5903-0.1962-0.81220.4992-0.27041.62640.12650.1446-0.1013-0.2685-0.0599-0.0189-0.1556-0.0201-0.05960.34220.0867-0.04480.3049-0.12930.3428110.26917.472134.3015
1260.33540.3798-0.21851.9322-0.30420.68190.19130.01530.4015-0.082-0.09010.4195-0.4827-0.0277-0.11790.42630.06670.04420.3139-0.06270.4748118.655127.568737.826
1271.21620.3990.18720.6732-0.57231.91090.044-0.1001-0.0081-0.04960.078-0.1339-0.03990.1112-0.13160.26130.0182-0.00410.2934-0.07470.3379128.277614.468745.6228
1280.7999-0.1412-0.19620.55150.28310.75620.03830.1038-0.10110.10010.03430.01640.1174-0.0601-0.04670.308-0.0443-0.06280.2690.02610.270298.88946.2061-44.6573
1291.8420.2448-0.34941.85480.13161.51750.0772-0.04850.14590.1669-0.0547-0.0491-0.10190.1281-0.00940.3709-0.0369-0.01060.26510.04980.202898.462919.0794-24.8056
1301.5511-1.3294-0.6231.90460.37391.4519-0.2846-0.34670.18660.86860.2330.0259-0.12890.10060.04850.7899-0.0119-0.02410.46120.01630.33194.8427.4392-7.9834
1312.2132-0.4551-0.2991.5387-0.08711.5218-0.5296-0.73890.50011.48090.5368-0.4666-0.3584-0.0705-0.10211.11340.08350.00130.6105-0.08720.374886.076636.1003-0.2432
1321.5108-0.9857-0.39682.1387-0.16471.1242-0.6664-1.0199-0.23411.00490.61240.11750.1207-0.0838-0.08071.18340.21150.35860.70280.17380.239578.046126.70960.0707
1331.366-0.8406-0.28711.00880.36920.4553-0.2329-0.41-0.14020.82860.08850.3082-0.00850.0256-0.11430.76210.01390.13430.4260.09640.357681.641222.3429-7.7622
1342.003-1.4974-0.51421.77750.38310.93870.119-0.27180.27050.46140.0066-0.15070.03520.2099-0.02180.5375-0.0699-0.08660.37090.0590.2784104.22313.7094-18.383
1351.44640.3401-1.00681.2634-0.06541.60380.0436-0.1988-0.15550.327-0.0057-0.1833-0.06270.1385-0.04030.4054-0.0209-0.13320.30710.04930.3432113.06638.0938-29.2307
1362.42430.6827-0.5951.16610.5122.49410.08290.0571-0.07860.1459-0.02950.02350.0808-0.0018-0.03330.3371-0.0207-0.08340.24550.01540.2981105.2735.2608-37.3198
1371.62760.1765-0.07511.31751.50851.81370.18430.09940.1266-0.0043-0.2809-0.0985-0.2568-0.2814-0.00980.33270.014-0.03540.31220.04860.275298.621614.6095-38.2
1380.6753-0.02790.17073.6016-1.35420.94040.17320.54470.7821-0.3067-0.3374-0.4972-0.33260.36590.06720.5272-0.03090.01260.47530.11760.555997.563635.8838-31.8208
1391.7750.1143-0.40770.76240.95072.40720.05050.1895-0.15240.05910.01080.04050.1743-0.1739-0.0580.2475-0.0093-0.06330.22620.02380.22591.480610.1467-42.9549
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 82 )A7 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 155 )A83 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 215 )A156 - 215
4X-RAY DIFFRACTION4chain 'A' and (resid 216 through 260 )A216 - 260
5X-RAY DIFFRACTION5chain 'A' and (resid 261 through 321 )A261 - 321
6X-RAY DIFFRACTION6chain 'A' and (resid 322 through 348 )A322 - 348
7X-RAY DIFFRACTION7chain 'A' and (resid 349 through 372 )A349 - 372
8X-RAY DIFFRACTION8chain 'A' and (resid 373 through 438 )A373 - 438
9X-RAY DIFFRACTION9chain 'A' and (resid 439 through 478 )A439 - 478
10X-RAY DIFFRACTION10chain 'B' and (resid 7 through 82 )B7 - 82
11X-RAY DIFFRACTION11chain 'B' and (resid 83 through 155 )B83 - 155
12X-RAY DIFFRACTION12chain 'B' and (resid 156 through 233 )B156 - 233
13X-RAY DIFFRACTION13chain 'B' and (resid 234 through 260 )B234 - 260
14X-RAY DIFFRACTION14chain 'B' and (resid 261 through 321 )B261 - 321
15X-RAY DIFFRACTION15chain 'B' and (resid 322 through 348 )B322 - 348
16X-RAY DIFFRACTION16chain 'B' and (resid 349 through 372 )B349 - 372
17X-RAY DIFFRACTION17chain 'B' and (resid 373 through 438 )B373 - 438
18X-RAY DIFFRACTION18chain 'B' and (resid 439 through 480 )B439 - 480
19X-RAY DIFFRACTION19chain 'C' and (resid 7 through 82 )C7 - 82
20X-RAY DIFFRACTION20chain 'C' and (resid 83 through 186 )C83 - 186
21X-RAY DIFFRACTION21chain 'C' and (resid 187 through 215 )C187 - 215
22X-RAY DIFFRACTION22chain 'C' and (resid 216 through 260 )C216 - 260
23X-RAY DIFFRACTION23chain 'C' and (resid 261 through 297 )C261 - 297
24X-RAY DIFFRACTION24chain 'C' and (resid 298 through 360 )C298 - 360
25X-RAY DIFFRACTION25chain 'C' and (resid 361 through 438 )C361 - 438
26X-RAY DIFFRACTION26chain 'C' and (resid 439 through 478 )C439 - 478
27X-RAY DIFFRACTION27chain 'D' and (resid 7 through 82 )D7 - 82
28X-RAY DIFFRACTION28chain 'D' and (resid 83 through 297 )D83 - 297
29X-RAY DIFFRACTION29chain 'D' and (resid 298 through 372 )D298 - 372
30X-RAY DIFFRACTION30chain 'D' and (resid 373 through 478 )D373 - 478
31X-RAY DIFFRACTION31chain 'E' and (resid 7 through 43 )E7 - 43
32X-RAY DIFFRACTION32chain 'E' and (resid 44 through 82 )E44 - 82
33X-RAY DIFFRACTION33chain 'E' and (resid 83 through 125 )E83 - 125
34X-RAY DIFFRACTION34chain 'E' and (resid 126 through 155 )E126 - 155
35X-RAY DIFFRACTION35chain 'E' and (resid 156 through 186 )E156 - 186
36X-RAY DIFFRACTION36chain 'E' and (resid 187 through 215 )E187 - 215
37X-RAY DIFFRACTION37chain 'E' and (resid 216 through 260 )E216 - 260
38X-RAY DIFFRACTION38chain 'E' and (resid 261 through 321 )E261 - 321
39X-RAY DIFFRACTION39chain 'E' and (resid 322 through 348 )E322 - 348
40X-RAY DIFFRACTION40chain 'E' and (resid 349 through 372 )E349 - 372
41X-RAY DIFFRACTION41chain 'E' and (resid 373 through 438 )E373 - 438
42X-RAY DIFFRACTION42chain 'E' and (resid 439 through 478 )E439 - 478
43X-RAY DIFFRACTION43chain 'F' and (resid 7 through 82 )F7 - 82
44X-RAY DIFFRACTION44chain 'F' and (resid 83 through 125 )F83 - 125
45X-RAY DIFFRACTION45chain 'F' and (resid 126 through 155 )F126 - 155
46X-RAY DIFFRACTION46chain 'F' and (resid 156 through 186 )F156 - 186
47X-RAY DIFFRACTION47chain 'F' and (resid 187 through 215 )F187 - 215
48X-RAY DIFFRACTION48chain 'F' and (resid 216 through 260 )F216 - 260
49X-RAY DIFFRACTION49chain 'F' and (resid 261 through 297 )F261 - 297
50X-RAY DIFFRACTION50chain 'F' and (resid 298 through 321 )F298 - 321
51X-RAY DIFFRACTION51chain 'F' and (resid 322 through 348 )F322 - 348
52X-RAY DIFFRACTION52chain 'F' and (resid 349 through 372 )F349 - 372
53X-RAY DIFFRACTION53chain 'F' and (resid 373 through 438 )F373 - 438
54X-RAY DIFFRACTION54chain 'F' and (resid 439 through 478 )F439 - 478
55X-RAY DIFFRACTION55chain 'G' and (resid 7 through 43 )G7 - 43
56X-RAY DIFFRACTION56chain 'G' and (resid 44 through 125 )G44 - 125
57X-RAY DIFFRACTION57chain 'G' and (resid 126 through 161 )G126 - 161
58X-RAY DIFFRACTION58chain 'G' and (resid 162 through 215 )G162 - 215
59X-RAY DIFFRACTION59chain 'G' and (resid 216 through 260 )G216 - 260
60X-RAY DIFFRACTION60chain 'G' and (resid 261 through 321 )G261 - 321
61X-RAY DIFFRACTION61chain 'G' and (resid 322 through 348 )G322 - 348
62X-RAY DIFFRACTION62chain 'G' and (resid 349 through 372 )G349 - 372
63X-RAY DIFFRACTION63chain 'G' and (resid 373 through 438 )G373 - 438
64X-RAY DIFFRACTION64chain 'G' and (resid 439 through 478 )G439 - 478
65X-RAY DIFFRACTION65chain 'H' and (resid 7 through 82 )H7 - 82
66X-RAY DIFFRACTION66chain 'H' and (resid 83 through 125 )H83 - 125
67X-RAY DIFFRACTION67chain 'H' and (resid 126 through 155 )H126 - 155
68X-RAY DIFFRACTION68chain 'H' and (resid 156 through 215 )H156 - 215
69X-RAY DIFFRACTION69chain 'H' and (resid 216 through 260 )H216 - 260
70X-RAY DIFFRACTION70chain 'H' and (resid 261 through 321 )H261 - 321
71X-RAY DIFFRACTION71chain 'H' and (resid 322 through 372 )H322 - 372
72X-RAY DIFFRACTION72chain 'H' and (resid 373 through 438 )H373 - 438
73X-RAY DIFFRACTION73chain 'H' and (resid 439 through 478 )H439 - 478
74X-RAY DIFFRACTION74chain 'I' and (resid 7 through 82 )I7 - 82
75X-RAY DIFFRACTION75chain 'I' and (resid 83 through 199 )I83 - 199
76X-RAY DIFFRACTION76chain 'I' and (resid 200 through 260 )I200 - 260
77X-RAY DIFFRACTION77chain 'I' and (resid 261 through 321 )I261 - 321
78X-RAY DIFFRACTION78chain 'I' and (resid 322 through 348 )I322 - 348
79X-RAY DIFFRACTION79chain 'I' and (resid 349 through 372 )I349 - 372
80X-RAY DIFFRACTION80chain 'I' and (resid 373 through 438 )I373 - 438
81X-RAY DIFFRACTION81chain 'I' and (resid 439 through 478 )I439 - 478
82X-RAY DIFFRACTION82chain 'J' and (resid 7 through 82 )J7 - 82
83X-RAY DIFFRACTION83chain 'J' and (resid 83 through 186 )J83 - 186
84X-RAY DIFFRACTION84chain 'J' and (resid 187 through 215 )J187 - 215
85X-RAY DIFFRACTION85chain 'J' and (resid 216 through 260 )J216 - 260
86X-RAY DIFFRACTION86chain 'J' and (resid 261 through 297 )J261 - 297
87X-RAY DIFFRACTION87chain 'J' and (resid 298 through 348 )J298 - 348
88X-RAY DIFFRACTION88chain 'J' and (resid 349 through 372 )J349 - 372
89X-RAY DIFFRACTION89chain 'J' and (resid 373 through 438 )J373 - 438
90X-RAY DIFFRACTION90chain 'J' and (resid 439 through 478 )J439 - 478
91X-RAY DIFFRACTION91chain 'K' and (resid 7 through 82 )K7 - 82
92X-RAY DIFFRACTION92chain 'K' and (resid 83 through 125 )K83 - 125
93X-RAY DIFFRACTION93chain 'K' and (resid 126 through 186 )K126 - 186
94X-RAY DIFFRACTION94chain 'K' and (resid 187 through 297 )K187 - 297
95X-RAY DIFFRACTION95chain 'K' and (resid 298 through 372 )K298 - 372
96X-RAY DIFFRACTION96chain 'K' and (resid 373 through 438 )K373 - 438
97X-RAY DIFFRACTION97chain 'K' and (resid 439 through 478 )K439 - 478
98X-RAY DIFFRACTION98chain 'L' and (resid 7 through 103 )L7 - 103
99X-RAY DIFFRACTION99chain 'L' and (resid 104 through 161 )L104 - 161
100X-RAY DIFFRACTION100chain 'L' and (resid 162 through 186 )L162 - 186
101X-RAY DIFFRACTION101chain 'L' and (resid 187 through 215 )L187 - 215
102X-RAY DIFFRACTION102chain 'L' and (resid 216 through 260 )L216 - 260
103X-RAY DIFFRACTION103chain 'L' and (resid 261 through 335 )L261 - 335
104X-RAY DIFFRACTION104chain 'L' and (resid 336 through 360 )L336 - 360
105X-RAY DIFFRACTION105chain 'L' and (resid 361 through 438 )L361 - 438
106X-RAY DIFFRACTION106chain 'L' and (resid 439 through 478 )L439 - 478
107X-RAY DIFFRACTION107chain 'M' and (resid 7 through 82 )M7 - 82
108X-RAY DIFFRACTION108chain 'M' and (resid 83 through 125 )M83 - 125
109X-RAY DIFFRACTION109chain 'M' and (resid 126 through 215 )M126 - 215
110X-RAY DIFFRACTION110chain 'M' and (resid 216 through 260 )M216 - 260
111X-RAY DIFFRACTION111chain 'M' and (resid 261 through 321 )M261 - 321
112X-RAY DIFFRACTION112chain 'M' and (resid 322 through 348 )M322 - 348
113X-RAY DIFFRACTION113chain 'M' and (resid 349 through 438 )M349 - 438
114X-RAY DIFFRACTION114chain 'M' and (resid 439 through 478 )M439 - 478
115X-RAY DIFFRACTION115chain 'N' and (resid 7 through 125 )N7 - 125
116X-RAY DIFFRACTION116chain 'N' and (resid 126 through 215 )N126 - 215
117X-RAY DIFFRACTION117chain 'N' and (resid 216 through 260 )N216 - 260
118X-RAY DIFFRACTION118chain 'N' and (resid 261 through 321 )N261 - 321
119X-RAY DIFFRACTION119chain 'N' and (resid 322 through 348 )N322 - 348
120X-RAY DIFFRACTION120chain 'N' and (resid 349 through 438 )N349 - 438
121X-RAY DIFFRACTION121chain 'N' and (resid 439 through 478 )N439 - 478
122X-RAY DIFFRACTION122chain 'O' and (resid 7 through 125 )O7 - 125
123X-RAY DIFFRACTION123chain 'O' and (resid 126 through 215 )O126 - 215
124X-RAY DIFFRACTION124chain 'O' and (resid 216 through 260 )O216 - 260
125X-RAY DIFFRACTION125chain 'O' and (resid 261 through 348 )O261 - 348
126X-RAY DIFFRACTION126chain 'O' and (resid 349 through 438 )O349 - 438
127X-RAY DIFFRACTION127chain 'O' and (resid 439 through 478 )O439 - 478
128X-RAY DIFFRACTION128chain 'P' and (resid 7 through 43 )P7 - 43
129X-RAY DIFFRACTION129chain 'P' and (resid 44 through 82 )P44 - 82
130X-RAY DIFFRACTION130chain 'P' and (resid 83 through 125 )P83 - 125
131X-RAY DIFFRACTION131chain 'P' and (resid 126 through 155 )P126 - 155
132X-RAY DIFFRACTION132chain 'P' and (resid 156 through 186 )P156 - 186
133X-RAY DIFFRACTION133chain 'P' and (resid 187 through 215 )P187 - 215
134X-RAY DIFFRACTION134chain 'P' and (resid 216 through 260 )P216 - 260
135X-RAY DIFFRACTION135chain 'P' and (resid 261 through 321 )P261 - 321
136X-RAY DIFFRACTION136chain 'P' and (resid 322 through 348 )P322 - 348
137X-RAY DIFFRACTION137chain 'P' and (resid 349 through 372 )P349 - 372
138X-RAY DIFFRACTION138chain 'P' and (resid 373 through 438 )P373 - 438
139X-RAY DIFFRACTION139chain 'P' and (resid 439 through 478 )P439 - 478

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る