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- PDB-7r3a: Crystal structure of S-adenosyl-L-homocysteine hydrolase from Met... -

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基本情報

登録情報
データベース: PDB / ID: 7r3a
タイトルCrystal structure of S-adenosyl-L-homocysteine hydrolase from Methanococcus maripaludis in complex with inosine
要素S-inosyl-L-homocysteine hydrolase
キーワードHYDROLASE / Complex / S-adenosyl-L-homocysteine (SAH) / S-adenosyl-L-methionine (SAM)
機能・相同性
機能・相同性情報


S-inosyl-L-homocysteine hydrolase / trialkylsulfonium hydrolase activity / S-adenosylmethionine biosynthetic process / one-carbon metabolic process / cytoplasm
類似検索 - 分子機能
Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain ...Adenosylhomocysteinase-like / S-adenosyl-L-homocysteine hydrolase, conserved site / Adenosylhomocysteinase-like superfamily / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase signature 1. / S-adenosyl-L-homocysteine hydrolase signature 2. / S-adenosyl-L-homocysteine hydrolase / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / S-adenosyl-L-homocysteine hydrolase, NAD binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / INOSINE / S-inosyl-L-homocysteine hydrolase
類似検索 - 構成要素
生物種Methanococcus maripaludis (古細菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.53 Å
データ登録者Saleem-Batcha, R. / Popadic, D. / Andexer, J.N.
資金援助 ドイツ, 2件
組織認可番号国
German Research Foundation (DFG)235777276/RTG1976 ドイツ
European Research Council (ERC)ERC project 716966 ドイツ
引用ジャーナル: Commun Biol / 年: 2024
タイトル: Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases.
著者: Koeppl, L.H. / Popadic, D. / Saleem-Batcha, R. / Germer, P. / Andexer, J.N.
履歴
登録2022年2月6日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年2月15日Provider: repository / タイプ: Initial release
改定 1.12024年2月7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
改定 1.22024年9月18日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: S-inosyl-L-homocysteine hydrolase
B: S-inosyl-L-homocysteine hydrolase
C: S-inosyl-L-homocysteine hydrolase
D: S-inosyl-L-homocysteine hydrolase
E: S-inosyl-L-homocysteine hydrolase
F: S-inosyl-L-homocysteine hydrolase
G: S-inosyl-L-homocysteine hydrolase
H: S-inosyl-L-homocysteine hydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)393,50132
ポリマ－384,4948
非ポリマー9,00724
水1,69394
1
A: S-inosyl-L-homocysteine hydrolase
E: S-inosyl-L-homocysteine hydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,3758
ポリマ－96,1242
非ポリマー2,2526
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: S-inosyl-L-homocysteine hydrolase
D: S-inosyl-L-homocysteine hydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,3758
ポリマ－96,1242
非ポリマー2,2526
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: S-inosyl-L-homocysteine hydrolase
H: S-inosyl-L-homocysteine hydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,3758
ポリマ－96,1242
非ポリマー2,2526
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
F: S-inosyl-L-homocysteine hydrolase
G: S-inosyl-L-homocysteine hydrolase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)98,3758
ポリマ－96,1242
非ポリマー2,2526
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)65.775, 328.867, 85.094
Angle α, β, γ (deg.)90.000, 107.230, 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 22 through 37 or resid 39...
21(chain C and (resid 22 through 37 or resid 39...
31(chain E and (resid 22 through 37 or resid 39...
41(chain H and (resid 22 through 37 or resid 39...
12(chain B and (resid 22 through 274 or resid 276...
22(chain F and (resid 22 through 274 or resid 276...
13(chain D and (resid 22 through 87 or resid 89...
23(chain G and (resid 22 through 87 or resid 89...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111SERSERMETMET(chain A and (resid 22 through 37 or resid 39...AA22 - 3722 - 37
121TRPTRPASNASN(chain A and (resid 22 through 37 or resid 39...AA39 - 12239 - 122
131GLUGLUMETMET(chain A and (resid 22 through 37 or resid 39...AA124 - 274124 - 274
141GLUGLULEULEU(chain A and (resid 22 through 37 or resid 39...AA276 - 294276 - 294
151METMETSERSER(chain A and (resid 22 through 37 or resid 39...AA296 - 327296 - 327
161SERSERTYRTYR(chain A and (resid 22 through 37 or resid 39...AA329 - 399329 - 399
171GLNGLNGLNGLN(chain A and (resid 22 through 37 or resid 39...AA401 - 424401 - 424
181LYSLYSASPASP(chain A and (resid 22 through 37 or resid 39...AA426 - 430426 - 430
191NOSNOSPG4PG4(chain A and (resid 22 through 37 or resid 39...AI - K501 - 503
211SERSERMETMET(chain C and (resid 22 through 37 or resid 39...CC22 - 3722 - 37
221TRPTRPASNASN(chain C and (resid 22 through 37 or resid 39...CC39 - 12239 - 122
231GLUGLUMETMET(chain C and (resid 22 through 37 or resid 39...CC124 - 274124 - 274
241GLUGLULEULEU(chain C and (resid 22 through 37 or resid 39...CC276 - 294276 - 294
251SERSERLYSLYS(chain C and (resid 22 through 37 or resid 39...CC22 - 43222 - 432
261SERSERTYRTYR(chain C and (resid 22 through 37 or resid 39...CC329 - 399329 - 399
271GLNGLNGLNGLN(chain C and (resid 22 through 37 or resid 39...CC401 - 424401 - 424
281LYSLYSASPASP(chain C and (resid 22 through 37 or resid 39...CC426 - 430426 - 430
291NOSNOSPG4PG4(chain C and (resid 22 through 37 or resid 39...CO - Q501 - 503
311SERSERMETMET(chain E and (resid 22 through 37 or resid 39...EE22 - 3722 - 37
321TRPTRPASNASN(chain E and (resid 22 through 37 or resid 39...EE39 - 12239 - 122
331GLUGLUMETMET(chain E and (resid 22 through 37 or resid 39...EE124 - 274124 - 274
341GLUGLULEULEU(chain E and (resid 22 through 37 or resid 39...EE276 - 294276 - 294
351METMETSERSER(chain E and (resid 22 through 37 or resid 39...EE296 - 327296 - 327
361SERSERTYRTYR(chain E and (resid 22 through 37 or resid 39...EE329 - 399329 - 399
371GLNGLNGLNGLN(chain E and (resid 22 through 37 or resid 39...EE401 - 424401 - 424
381LYSLYSASPASP(chain E and (resid 22 through 37 or resid 39...EE426 - 430426 - 430
391PG4PG4NADNAD(chain E and (resid 22 through 37 or resid 39...EU - W501 - 503
411SERSERMETMET(chain H and (resid 22 through 37 or resid 39...HH22 - 3722 - 37
421TRPTRPASNASN(chain H and (resid 22 through 37 or resid 39...HH39 - 12239 - 122
431GLUGLUMETMET(chain H and (resid 22 through 37 or resid 39...HH124 - 274124 - 274
441GLUGLULEULEU(chain H and (resid 22 through 37 or resid 39...HH276 - 294276 - 294
451SERSERLYSLYS(chain H and (resid 22 through 37 or resid 39...HH22 - 43222 - 432
461SERSERTYRTYR(chain H and (resid 22 through 37 or resid 39...HH329 - 399329 - 399
471GLNGLNGLNGLN(chain H and (resid 22 through 37 or resid 39...HH401 - 424401 - 424
481LYSLYSASPASP(chain H and (resid 22 through 37 or resid 39...HH426 - 430426 - 430
491PG4PG4NADNAD(chain H and (resid 22 through 37 or resid 39...HDA - FA501 - 503
112SERSERMETMET(chain B and (resid 22 through 274 or resid 276...BB22 - 27422 - 274
122GLUGLUSERSER(chain B and (resid 22 through 274 or resid 276...BB276 - 327276 - 327
132SERSERGLYGLY(chain B and (resid 22 through 274 or resid 276...BB329 - 388329 - 388
142LEULEUTYRTYR(chain B and (resid 22 through 274 or resid 276...BB390 - 399390 - 399
152GLNGLNLYSLYS(chain B and (resid 22 through 274 or resid 276...BB401 - 432401 - 432
162NOSNOSNADNAD(chain B and (resid 22 through 274 or resid 276...BL - M501 - 502
212SERSERMETMET(chain F and (resid 22 through 274 or resid 276...FF22 - 27422 - 274
222GLUGLUSERSER(chain F and (resid 22 through 274 or resid 276...FF276 - 327276 - 327
232SERSERGLYGLY(chain F and (resid 22 through 274 or resid 276...FF329 - 388329 - 388
242LEULEUTYRTYR(chain F and (resid 22 through 274 or resid 276...FF390 - 399390 - 399
252GLNGLNLYSLYS(chain F and (resid 22 through 274 or resid 276...FF401 - 432401 - 432
262PG4PG4NOSNOS(chain F and (resid 22 through 274 or resid 276...FX - Y501 - 502
113SERSERALAALA(chain D and (resid 22 through 87 or resid 89...DD22 - 8722 - 87
123ILEILEGLYGLY(chain D and (resid 22 through 87 or resid 89...DD89 - 16089 - 160
133ILEILELEULEU(chain D and (resid 22 through 87 or resid 89...DD162 - 294162 - 294
143METMETTRPTRP(chain D and (resid 22 through 87 or resid 89...DD296 - 431296 - 431
153NOSNOSNADNAD(chain D and (resid 22 through 87 or resid 89...DR - S501 - 502
213SERSERALAALA(chain G and (resid 22 through 87 or resid 89...GG22 - 8722 - 87
223ILEILEGLYGLY(chain G and (resid 22 through 87 or resid 89...GG89 - 16089 - 160
233ILEILELEULEU(chain G and (resid 22 through 87 or resid 89...GG162 - 294162 - 294
243SERSERLYSLYS(chain G and (resid 22 through 87 or resid 89...GG22 - 43222 - 432

NCSアンサンブル:
ID
1
2
3

NCS oper:
IDCodeMatrixベクター
1given(-0.957687307775, 0.28736359944, 0.0160369025605), (0.287083731804, 0.949826173666, 0.12414979159), (0.0204438611843, 0.123500613502, -0.992133885625)28.0329498761, 0.581293188169, 101.549244552
2given(-0.9305870042, -0.034843715258, 0.364408758294), (-0.0337759824582, -0.98304094818, -0.180248931234), (0.364509273714, -0.180045576755, 0.913628250257)-8.91844448409, 49.1463575309, 6.3245716094
3given(0.889137919729, -0.255177603422, -0.379892287907), (-0.250970608006, -0.966038971079, 0.0615017095133), (-0.38268461377, 0.0406582964162, -0.922983959403)50.7663793107, 45.2171486314, 101.635134045
4given(-0.935721238562, 0.350347952801, 0.0410131158571), (0.348815594997, 0.901737953587, 0.255335747101), (0.0524732731104, 0.253229095937, -0.965982184401)2.80973719398, -13.1469294695, 47.716109879
5given(-0.934399907668, 0.353255015713, 0.0459097639266), (0.352944801118, 0.9006214973, 0.253595910782), (0.0482367071197, 0.253163608118, -0.966220165185)2.20553871166, -12.9440988418, 47.8478620781

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要素

#1: タンパク質
S-inosyl-L-homocysteine hydrolase / SIHH


分子量: 48061.809 Da / 分子数: 8 / 由来タイプ: 組換発現
由来: (組換発現) Methanococcus maripaludis (古細菌)
株: S2 / LL / 遺伝子: ahcY, MMP0920 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: Q6LYR8, S-inosyl-L-homocysteine hydrolase
#2: 化合物
ChemComp-NOS / INOSINE


分子量: 268.226 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C10H12N4O5 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


分子量: 663.425 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C21H27N7O14P2 / タイプ: SUBJECT OF INVESTIGATION / コメント: NAD*YM
#4: 化合物
ChemComp-PG4 / TETRAETHYLENE GLYCOL


分子量: 194.226 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C8H18O5 / コメント: 沈殿剤*YM
#5: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 94 / 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: 2.29 Å3/Da / 溶媒含有率: 46.2 %
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 / pH: 8 / 詳細: 28% (w/v) PEG 3350,100 mM MMT buffer pH 8.0

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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: SLS / ビームライン: X06SA / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2021年3月13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: 1 Å / 相対比: 1
反射解像度: 2.53→48.76 Å / Num. obs: 111512 / % possible obs: 97.5 % / 冗長度: 3.6 % / Biso Wilson estimate: 47.75 Å2 / CC1/2: 0.98 / Rmerge(I) obs: 0.19 / Net I/σ(I): 5.9
反射 シェル解像度: 2.53→2.67 Å / Num. unique obs: 16348 / CC1/2: 0.4

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.1_4122精密化
XDSデータ削減
SCALA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: 1V8B

1v8b


解像度: 2.53→47.86 Å / SU ML: 0.36 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 29.28 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2428 5569 5 %
Rwork0.1882 105754 -
obs0.1909 111323 97.38 %
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: 152.16 Å2 / Biso mean: 70.1313 Å2 / Biso min: 24.53 Å2
精密化ステップサイクル: final / 解像度: 2.53→47.86 Å
タンパク質核酸リガンド溶媒全体
原子数25440 0 608 94 26142
Biso mean--64.67 53.96 -
残基数----3288
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4896X-RAY DIFFRACTION4.644TORSIONAL
12C4896X-RAY DIFFRACTION4.644TORSIONAL
13E4896X-RAY DIFFRACTION4.644TORSIONAL
14H4896X-RAY DIFFRACTION4.644TORSIONAL
21B2473X-RAY DIFFRACTION4.644TORSIONAL
22F2473X-RAY DIFFRACTION4.644TORSIONAL
31D2483X-RAY DIFFRACTION4.644TORSIONAL
32G2483X-RAY DIFFRACTION4.644TORSIONAL
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 (%)
2.53-2.560.36681830.29293467365098
2.56-2.590.34911890.28823579376898
2.59-2.620.36371860.27943535372198
2.62-2.650.32711880.28893562375098
2.65-2.690.35211830.25983485366898
2.69-2.730.32571890.25113592378198
2.73-2.760.33171870.24813544373198
2.76-2.810.29221840.24113493367798
2.81-2.850.31731920.24833635382798
2.85-2.90.31731800.25763423360397
2.9-2.950.31341740.26123301347591
2.95-30.32651750.27933324349991
3-3.060.37591880.26823572376099
3.06-3.120.28681880.25593570375898
3.12-3.190.28681870.22593555374299
3.19-3.260.26341900.20753618380899
3.26-3.340.24871870.20863540372798
3.34-3.430.2961890.20293594378399
3.43-3.530.25261890.19513592378199
3.53-3.650.24521900.18843599378999
3.65-3.780.26641860.18833535372199
3.78-3.930.21621890.16183584377398
3.93-4.110.22691880.15913563375198
4.11-4.320.19451730.14283295346891
4.32-4.60.17171830.13043466364996
4.6-4.950.16891880.12983605379399
4.95-5.450.16431900.14493591378199
5.45-6.230.25551880.16643578376699
6.24-7.850.23281880.17063570375898
7.85-47.860.16511780.14833387356592
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)
10.2120.91340.69956.28951.11793.22470.1915-0.41971.0910.0763-0.0168-0.1164-0.6017-0.1662-0.18120.39860.03920.12190.4492-0.00870.924-5.125654.510326.0866
22.58140.750.43223.20982.13366.47060.243-0.76680.75920.8371-0.17250.2507-0.4319-0.6294-0.09920.57340.04510.09670.4838-0.12350.5353-8.703745.371440.4466
31.78071.32690.37253.3865-1.09573.09630.2096-0.18581.08890.54650.1132-0.1031-0.63930.0805-0.29510.431-0.00920.07170.4117-0.16030.83360.946252.180933.4448
42.37940.49210.46974.96010.11272.9060.1377-0.7210.83020.7934-0.2066-0.6728-0.28890.32830.12860.5212-0.0711-0.10490.6213-0.1620.660610.945643.96743.4146
53.48680.39042.10162.63221.19786.6542-0.0742-0.7982-0.20990.592-0.036-0.29650.17140.61840.22880.3969-0.0454-0.01990.52680.02650.36153.414531.282639.3874
61.48810.1560.12231.7615-0.27381.5690.21850.2710.1042-0.0856-0.1393-0.34980.14510.1651-0.05180.27070.07550.00760.3424-0.00890.45477.589826.224217.3223
73.0268-0.3401-0.7852.4468-0.37143.5895-0.02160.1663-0.17880.0413-0.1375-0.89070.29090.81110.07450.25930.0550.00620.43460.02850.705920.79530.623616.581
83.46820.3761-0.75881.6848-0.22431.86650.1263-0.03080.90130.0481-0.0493-0.4089-0.18430.3695-0.06320.27270.0130.06090.3880.00280.702917.813642.033617.4113
92.8490.54150.42742.99580.44651.97190.2041-0.6977-0.28270.6087-0.07710.25320.2304-0.1162-0.07780.40730.01570.06470.44710.05610.3909-9.92826.886940.6582
100.26890.1033-1.00732.94550.2763.8842-0.11170.65330.0726-0.7292-0.1185-0.170.16280.25290.22010.4853-0.0270.05050.6660.05840.43911.727896.537343.2067
112.3968-0.75870.5453.5773-0.10712.98750.17371.0352-0.6404-0.8632-0.23970.32810.455-0.04530.07390.5808-0.0444-0.00130.7334-0.19250.48116.241184.600545.5439
123.13180.17971.05233.42541.39423.7943-0.29640.8467-0.6551-0.42730.15550.80240.5513-0.62280.15820.5343-0.1246-0.02950.6099-0.15040.7901-4.777374.48253.5356
132.1134-0.6170.25372.5413-0.2671.319-0.28520.1204-0.25180.27850.36220.28920.1237-0.1257-0.07440.24820.00610.05730.30020.04730.33750.309193.824570.1832
143.4859-1.0156-0.08182.9547-0.21112.1225-0.18180.4379-0.2675-0.14730.26990.9289-0.0052-0.4897-0.09350.2673-0.0286-0.04380.46770.0890.58-12.4291101.713161.7163
152.63550.18840.36721.436-0.32562.1796-0.17510.1754-0.71540.09940.0957-0.09870.6140.14150.04320.4320.06230.11250.3584-0.03910.610516.644876.500566.9005
160.9040.50430.80383.7256-1.70632.05660.24580.54921.16890.0511-0.2550.014-0.17110.27990.0070.43950.0290.09410.7010.3140.926249.964554.00482.6064
170.02130.19270.10032.0953-0.1530.82620.37240.630.5426-0.74910.2377-0.7513-0.11090.9006-0.36720.70030.08150.26881.34370.33720.657850.982945.861167.2541
180.2080.51440.24621.53520.11351.2031-0.07830.79210.8388-0.37530.0656-0.115-0.39710.19940.04530.58670.06130.11550.96310.53281.022743.658654.442575.2403
190.5427-0.53940.12252.11340.93510.6784-0.00810.58450.3535-0.5003-0.17170.2128-0.35220.22110.16050.74760.22680.0911.32940.71211.196933.902855.799367.9721
200.117-0.1498-0.14182.6792-1.72691.7186-0.15471.61480.7281-0.75660.08950.0048-0.4149-0.08020.05690.75080.12460.03051.35980.43690.814230.123446.97862.0012
210.441-0.22940.97640.8776-1.12082.59040.17671.13120.2289-0.98060.1495-0.02870.1195-0.1606-0.29210.74750.15190.09571.09710.15650.420736.125335.671967.3369
221.70190.09520.33891.87290.011.08380.14960.43480.3323-0.2482-0.11940.20960.08430.1032-0.06860.29040.0801-0.01680.43110.03550.468729.481829.690888.1875
233.49620.033-1.40392.745-0.09982.05030.00840.52340.3496-0.15620.09480.66360.1817-0.3282-0.11350.25720.0776-0.00820.42820.09270.591118.169137.518989.6527
243.5462-0.668-0.0132.08680.44391.12150.08910.43490.8639-0.2871-0.11550.0682-0.2464-0.17730.00850.34590.04790.00220.43540.19810.764824.23347.578590.2955
251.41430.1756-1.42532.0683-0.68854.81730.11960.79720.2673-0.65990.0614-0.24820.14310.2229-0.11850.52760.1170.11670.88460.14240.483345.982339.583466.8582
260.8490.24340.18111.67910.11630.29660.02090.754-0.2275-0.66990.1375-0.21340.23750.3405-0.14810.77810.20020.15031.1191-0.05960.528947.324423.232363.7568
270.9575-0.09641.15713.6855-1.76835.0828-0.25980.79210.7488-0.4540.03660.115-0.1742-0.30140.15870.3969-0.0039-0.11570.65050.29960.8726-3.0264120.876349.3333
281.9547-0.2848-0.33332.8828-0.17731.5543-0.11360.42731.1470.01020.1253-0.233-0.5511-0.06890.00380.4022-0.0094-0.10760.46050.18450.934610.4537126.738361.6906
292.9031-0.6769-0.02852.4429-0.63782.2089-0.26750.42650.7526-0.0537-0.0025-0.5804-0.17070.33790.28150.2914-0.0348-0.07610.4820.13280.614625.2669111.327857.6228
301.1470.868-0.13517.64360.4861.94020.08970.01121.0674-0.0763-0.10550.1592-0.6453-0.4303-0.00920.53180.068-0.12760.4360.14491.00770.9226132.748666.9989
312.06570.4646-0.55251.7001-0.69782.4357-0.128-0.48920.99751.19410.4466-0.2991-0.44740.1295-0.27020.86640.2727-0.20420.5663-0.16491.032-0.3184132.151583.6096
320.25080.11970.17093.0657-0.30520.8502-0.10.0179-0.7389-0.65410.1762-0.25820.83460.1626-0.1471.06360.2374-0.24910.5483-0.15971.25173.2146-15.644617.8871
331.7714-0.1149-0.00162.39430.35092.32330.1901-0.3721-0.91810.271-0.0163-0.15260.87830.2252-0.1380.7030.0569-0.23630.44060.0970.89040.7193-8.577134.8965
342.1550.70910.332.11480.13592.2240.2246-0.006-0.6363-0.0579-0.04960.52270.4419-0.2009-0.16280.3595-0.0013-0.08140.28270.00330.6785-17.01988.894421.3939
352.4072-0.4998-0.24551.28160.2060.74060.10380.1986-0.93040.02390.08170.26870.29710.0358-0.17850.57580.0251-0.15420.3292-0.01760.825-7.0446-2.038324.1918
361.92190.7777-1.16541.7071-0.36171.63190.0823-0.48610.03430.4833-0.1501-0.4870.09960.60210.04730.47210.0909-0.21880.5365-0.03230.671216.020113.731134.9171
370.11930.1803-0.29140.2841-0.52491.56850.1836-0.45540.08170.4962-0.12450.2138-0.34450.0352-0.05551.73130.8540.50831.240.22390.285928.755488.797432.0473
380.6146-0.66140.35531.206-0.20980.766-0.2635-1.1343-0.14831.0060.310.82320.2897-0.1581-0.01271.36331.04480.65830.76460.54631.004224.983878.902625.3225
390.61130.02660.14230.79740.1010.5551-0.6665-0.6761-0.8361.16290.840.44680.05140.2833-0.06481.13110.55740.35060.79690.35410.777835.493470.753418.5065
401.4535-0.1261-0.27971.8517-0.28392.1938-0.3953-0.5594-0.12410.89520.2773-0.4115-0.06570.37140.08420.70940.2644-0.12340.53750.02780.457749.245691.41989.6877
411.7414-0.59760.31061.9733-1.21311.9455-0.3243-0.2107-0.6770.48310.34420.91510.3339-0.2769-0.0180.66910.20470.26080.5650.19910.955217.925178.40134.1224
420.5026-0.4745-0.28230.87260.56591.5967-0.1618-0.83960.59450.9320.0119-0.4674-0.82290.63350.12881.5620.2702-0.6081.2082-0.37921.032454.7502115.103327.0428
430.10960.281-0.03680.5564-0.05890.21330.0409-0.93440.20421.34420.29930.3024-0.7590.2221-0.15682.4760.8146-0.83071.2572-1.1240.409644.9273121.071632.7967
440.7042-0.3269-0.41421.37510.22990.2075-0.1404-0.99550.62010.78290.2512-0.2903-0.97730.1817-0.12761.58260.2497-0.38480.9181-0.49931.172541.4922130.859520.0817
450.5638-0.0562-0.28610.783-0.43811.3876-0.6646-0.71410.45551.39160.70750.1203-0.4935-0.2901-0.10881.23060.52980.07070.7481-0.05080.492424.6323110.314316.573
461.3286-0.1199-0.4621.40050.62762.0957-0.0906-0.3160.8880.66260.1997-0.6659-0.49170.293-0.00240.89830.0482-0.40680.6521-0.17611.102553.5939125.85366.2879
471.03551.45790.67833.84470.7532.9985-0.0590.6664-0.8154-0.3087-0.0920.22890.692-0.13370.10840.76930.0396-0.17370.6433-0.34681.126221.5792-11.153381.9063
480.22450.2675-0.41221.33720.3781.51320.6821.057-1.4424-0.5738-0.32620.61330.8536-0.3473-0.31330.97640.1793-0.45361.0136-0.53831.224919.3785-4.56471.5305
49-0.00410.0237-0.03130.242-0.32380.4102-0.21190.364-0.3059-0.5927-0.5409-0.08040.2658-0.13730.30691.43480.4497-0.46861.4958-0.91881.255431.0417-9.821263.7147
500.70360.82530.96961.52421.50541.549-0.48280.8139-0.5679-0.6875-0.00760.17770.3664-0.07370.46781.36180.3267-0.14151.5286-0.53980.828631.84941.403557.2874
511.5882-0.091-0.09391.47760.10081.65030.44840.9373-0.6868-0.6629-0.2341-0.04590.50530.2538-0.18420.68560.2534-0.09550.7464-0.26230.619142.72365.230278.4499
521.4109-0.2577-0.34262.0026-0.03751.4240.17330.99080.0557-0.6206-0.16460.2675-0.01820.02350.0110.5480.1136-0.22930.8335-0.03840.665818.245222.736669.2783
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 43 )A22 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 72 )A44 - 72
3X-RAY DIFFRACTION3chain 'A' and (resid 73 through 121 )A73 - 121
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 181 )A122 - 181
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 204 )A182 - 204
6X-RAY DIFFRACTION6chain 'A' and (resid 205 through 273 )A205 - 273
7X-RAY DIFFRACTION7chain 'A' and (resid 274 through 310 )A274 - 310
8X-RAY DIFFRACTION8chain 'A' and (resid 311 through 365 )A311 - 365
9X-RAY DIFFRACTION9chain 'A' and (resid 366 through 432 )A366 - 432
10X-RAY DIFFRACTION10chain 'B' and (resid 22 through 43 )B22 - 43
11X-RAY DIFFRACTION11chain 'B' and (resid 44 through 145 )B44 - 145
12X-RAY DIFFRACTION12chain 'B' and (resid 146 through 182 )B146 - 182
13X-RAY DIFFRACTION13chain 'B' and (resid 183 through 273 )B183 - 273
14X-RAY DIFFRACTION14chain 'B' and (resid 274 through 365 )B274 - 365
15X-RAY DIFFRACTION15chain 'B' and (resid 366 through 432 )B366 - 432
16X-RAY DIFFRACTION16chain 'C' and (resid 22 through 43 )C22 - 43
17X-RAY DIFFRACTION17chain 'C' and (resid 44 through 72 )C44 - 72
18X-RAY DIFFRACTION18chain 'C' and (resid 73 through 121 )C73 - 121
19X-RAY DIFFRACTION19chain 'C' and (resid 122 through 145 )C122 - 145
20X-RAY DIFFRACTION20chain 'C' and (resid 146 through 182 )C146 - 182
21X-RAY DIFFRACTION21chain 'C' and (resid 183 through 204 )C183 - 204
22X-RAY DIFFRACTION22chain 'C' and (resid 205 through 273 )C205 - 273
23X-RAY DIFFRACTION23chain 'C' and (resid 274 through 310 )C274 - 310
24X-RAY DIFFRACTION24chain 'C' and (resid 311 through 365 )C311 - 365
25X-RAY DIFFRACTION25chain 'C' and (resid 366 through 386 )C366 - 386
26X-RAY DIFFRACTION26chain 'C' and (resid 387 through 432 )C387 - 432
27X-RAY DIFFRACTION27chain 'D' and (resid 22 through 43 )D22 - 43
28X-RAY DIFFRACTION28chain 'D' and (resid 44 through 273 )D44 - 273
29X-RAY DIFFRACTION29chain 'D' and (resid 274 through 365 )D274 - 365
30X-RAY DIFFRACTION30chain 'D' and (resid 366 through 386 )D366 - 386
31X-RAY DIFFRACTION31chain 'D' and (resid 387 through 432 )D387 - 432
32X-RAY DIFFRACTION32chain 'E' and (resid 22 through 43 )E22 - 43
33X-RAY DIFFRACTION33chain 'E' and (resid 44 through 204 )E44 - 204
34X-RAY DIFFRACTION34chain 'E' and (resid 205 through 334 )E205 - 334
35X-RAY DIFFRACTION35chain 'E' and (resid 335 through 386 )E335 - 386
36X-RAY DIFFRACTION36chain 'E' and (resid 387 through 432 )E387 - 432
37X-RAY DIFFRACTION37chain 'F' and (resid 22 through 43 )F22 - 43
38X-RAY DIFFRACTION38chain 'F' and (resid 44 through 109 )F44 - 109
39X-RAY DIFFRACTION39chain 'F' and (resid 110 through 204 )F110 - 204
40X-RAY DIFFRACTION40chain 'F' and (resid 205 through 365 )F205 - 365
41X-RAY DIFFRACTION41chain 'F' and (resid 366 through 432 )F366 - 432
42X-RAY DIFFRACTION42chain 'G' and (resid 22 through 72 )G22 - 72
43X-RAY DIFFRACTION43chain 'G' and (resid 73 through 153 )G73 - 153
44X-RAY DIFFRACTION44chain 'G' and (resid 154 through 204 )G154 - 204
45X-RAY DIFFRACTION45chain 'G' and (resid 205 through 365 )G205 - 365
46X-RAY DIFFRACTION46chain 'G' and (resid 366 through 432 )G366 - 432
47X-RAY DIFFRACTION47chain 'H' and (resid 22 through 43 )H22 - 43
48X-RAY DIFFRACTION48chain 'H' and (resid 44 through 109 )H44 - 109
49X-RAY DIFFRACTION49chain 'H' and (resid 110 through 153 )H110 - 153
50X-RAY DIFFRACTION50chain 'H' and (resid 154 through 181 )H154 - 181
51X-RAY DIFFRACTION51chain 'H' and (resid 182 through 386 )H182 - 386
52X-RAY DIFFRACTION52chain 'H' and (resid 387 through 432 )H387 - 432

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万見について

-
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