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- PDB-7xdr: Crystal structure of a glucosylglycerol phosphorylase from Marino... -

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基本情報

登録情報
データベース: PDB / ID: 7xdr
タイトルCrystal structure of a glucosylglycerol phosphorylase from Marinobacter adhaerens
要素Glucosylglycerol phosphorylase
キーワードBIOSYNTHETIC PROTEIN / phosphorylase
機能・相同性
機能・相同性情報


glucosylglycerol phosphorylase (configuration-retaining) / glucosylglycerol metabolic process / 1,4-alpha-oligoglucan phosphorylase activity / glycosyltransferase activity
類似検索 - 分子機能
Sucrose/Glucosylglycerate phosphorylase-related / Sucrose phosphorylase / Oligo-1,6-glucosidase; domain 2 / Oligo-1,6-glucosidase; Domain 2 / Oligo-1,6-glucosidase, domain 2 / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Glycoside hydrolase superfamily / Alpha-Beta Complex / Alpha Beta
類似検索 - ドメイン・相同性
Glucosylglycerol phosphorylase
類似検索 - 構成要素
生物種Marinobacter adhaerens (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Wei, H.L. / Li, Q. / Yang, J.G. / Liu, W.D. / Sun, Y.X.
資金援助1件
組織認可番号国
Not funded
引用ジャーナル: Acs Catalysis / 年: 2022
タイトル: Protein Engineering of Glucosylglycerol Phosphorylase Facilitating Efficient and Highly Regio- and Stereoselective Glycosylation of Polyols in a Synthetic System.
著者: Zhang, T. / Liu, P. / Wei, H. / Sun, X. / Zeng, Y. / Zhang, X. / Cai, Y. / Cui, M. / Ma, H. / Liu, W. / Sun, Y. / Yang, J.
履歴
登録2022年3月28日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02023年2月8日Provider: repository / タイプ: Initial release
改定 1.12023年11月29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

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集合体

登録構造単位
A: Glucosylglycerol phosphorylase
B: Glucosylglycerol phosphorylase
C: Glucosylglycerol phosphorylase
D: Glucosylglycerol phosphorylase
E: Glucosylglycerol phosphorylase
F: Glucosylglycerol phosphorylase
G: Glucosylglycerol phosphorylase
H: Glucosylglycerol phosphorylase
I: Glucosylglycerol phosphorylase
J: Glucosylglycerol phosphorylase
K: Glucosylglycerol phosphorylase
L: Glucosylglycerol phosphorylase
M: Glucosylglycerol phosphorylase
N: Glucosylglycerol phosphorylase
O: Glucosylglycerol phosphorylase
P: Glucosylglycerol phosphorylase
Q: Glucosylglycerol phosphorylase
R: Glucosylglycerol phosphorylase


分子量 (理論値)分子数
合計 (水以外)987,89018
ポリマ－987,89018
非ポリマー00
水30,7701708
1
A: Glucosylglycerol phosphorylase
B: Glucosylglycerol phosphorylase
C: Glucosylglycerol phosphorylase
D: Glucosylglycerol phosphorylase
G: Glucosylglycerol phosphorylase
R: Glucosylglycerol phosphorylase


分子量 (理論値)分子数
合計 (水以外)329,2976
ポリマ－329,2976
非ポリマー00
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area15170 Å2
ΔGint-41 kcal/mol
Surface area96140 Å2
手法PISA
2
E: Glucosylglycerol phosphorylase
K: Glucosylglycerol phosphorylase
L: Glucosylglycerol phosphorylase

H: Glucosylglycerol phosphorylase

M: Glucosylglycerol phosphorylase

N: Glucosylglycerol phosphorylase


分子量 (理論値)分子数
合計 (水以外)329,2976
ポリマ－329,2976
非ポリマー00
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
crystal symmetry operation2_555-x,y+1/2,-z1
Buried area15200 Å2
ΔGint-45 kcal/mol
Surface area96340 Å2
手法PISA
3
F: Glucosylglycerol phosphorylase
J: Glucosylglycerol phosphorylase
O: Glucosylglycerol phosphorylase

I: Glucosylglycerol phosphorylase

Q: Glucosylglycerol phosphorylase

P: Glucosylglycerol phosphorylase


分子量 (理論値)分子数
合計 (水以外)329,2976
ポリマ－329,2976
非ポリマー00
水1086
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
crystal symmetry operation2_756-x+2,y+1/2,-z+11
crystal symmetry operation2_646-x+1,y-1/2,-z+11
Buried area15030 Å2
ΔGint-47 kcal/mol
Surface area96400 Å2
手法PISA
単位格子
Length a, b, c (Å)102.267, 185.174, 257.619
Angle α, β, γ (deg.)90.000, 101.560, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 2 through 321 or (resid 322...
21(chain B and (resid 2 through 321 or (resid 322...
31(chain C and (resid 2 through 321 or (resid 322...
41(chain D and (resid 2 through 321 or (resid 322...
51(chain E and (resid 2 through 321 or (resid 322...
61(chain F and resid 2 through 480)
71(chain G and (resid 2 through 321 or (resid 322...
81(chain H and (resid 2 through 321 or (resid 322...
91(chain I and (resid 2 through 321 or (resid 322...
101(chain J and (resid 2 through 321 or (resid 322...
111(chain K and (resid 2 through 321 or (resid 322...
121(chain L and (resid 2 through 321 or (resid 322...
131(chain M and (resid 2 through 321 or (resid 322...
141(chain N and (resid 2 through 321 or (resid 322...
151(chain O and (resid 2 through 321 or (resid 322...
161(chain P and (resid 2 through 321 or (resid 322...
171(chain Q and (resid 2 through 321 or (resid 322...
181(chain R and (resid 2 through 321 or (resid 322...

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
11LEULEUMETMET(chain A and (resid 2 through 321 or (resid 322...AA2 - 3212 - 321
12ARGARGARGARG(chain A and (resid 2 through 321 or (resid 322...AA322 - 323322 - 323
13METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
14METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
15METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
16METMETCYSCYS(chain A and (resid 2 through 321 or (resid 322...AA1 - 4801 - 480
21LEULEUMETMET(chain B and (resid 2 through 321 or (resid 322...BB2 - 3212 - 321
22ARGARGARGARG(chain B and (resid 2 through 321 or (resid 322...BB322 - 323322 - 323
23METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
24METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
25METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
26METMETCYSCYS(chain B and (resid 2 through 321 or (resid 322...BB1 - 4801 - 480
31LEULEUMETMET(chain C and (resid 2 through 321 or (resid 322...CC2 - 3212 - 321
32ARGARGARGARG(chain C and (resid 2 through 321 or (resid 322...CC322 - 323322 - 323
33METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
34METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
35METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
36METMETCYSCYS(chain C and (resid 2 through 321 or (resid 322...CC1 - 4801 - 480
41LEULEUMETMET(chain D and (resid 2 through 321 or (resid 322...DD2 - 3212 - 321
42ARGARGARGARG(chain D and (resid 2 through 321 or (resid 322...DD322 - 323322 - 323
43METMETCYSCYS(chain D and (resid 2 through 321 or (resid 322...DD1 - 4801 - 480
44METMETCYSCYS(chain D and (resid 2 through 321 or (resid 322...DD1 - 4801 - 480
51LEULEUMETMET(chain E and (resid 2 through 321 or (resid 322...EE2 - 3212 - 321
52ARGARGARGARG(chain E and (resid 2 through 321 or (resid 322...EE322 - 323322 - 323
53LEULEUCYSCYS(chain E and (resid 2 through 321 or (resid 322...EE2 - 4802 - 480
54LEULEUCYSCYS(chain E and (resid 2 through 321 or (resid 322...EE2 - 4802 - 480
61LEULEUCYSCYS(chain F and resid 2 through 480)FF2 - 4802 - 480
71LEULEUMETMET(chain G and (resid 2 through 321 or (resid 322...GG2 - 3212 - 321
72ARGARGARGARG(chain G and (resid 2 through 321 or (resid 322...GG322 - 323322 - 323
73LEULEUCYSCYS(chain G and (resid 2 through 321 or (resid 322...GG2 - 4802 - 480
74LEULEUCYSCYS(chain G and (resid 2 through 321 or (resid 322...GG2 - 4802 - 480
81LEULEUMETMET(chain H and (resid 2 through 321 or (resid 322...HH2 - 3212 - 321
82ARGARGARGARG(chain H and (resid 2 through 321 or (resid 322...HH322 - 323322 - 323
83METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
84METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
85METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
86METMETCYSCYS(chain H and (resid 2 through 321 or (resid 322...HH1 - 4801 - 480
91LEULEUMETMET(chain I and (resid 2 through 321 or (resid 322...II2 - 3212 - 321
92ARGARGARGARG(chain I and (resid 2 through 321 or (resid 322...II322 - 323322 - 323
93METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
94METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
95METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
96METMETCYSCYS(chain I and (resid 2 through 321 or (resid 322...II1 - 4801 - 480
101LEULEUMETMET(chain J and (resid 2 through 321 or (resid 322...JJ2 - 3212 - 321
102ARGARGARGARG(chain J and (resid 2 through 321 or (resid 322...JJ322 - 323322 - 323
103METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
104METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
105METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
106METMETCYSCYS(chain J and (resid 2 through 321 or (resid 322...JJ1 - 4801 - 480
111LEULEUMETMET(chain K and (resid 2 through 321 or (resid 322...KK2 - 3212 - 321
112ARGARGARGARG(chain K and (resid 2 through 321 or (resid 322...KK322 - 323322 - 323
113METMETCYSCYS(chain K and (resid 2 through 321 or (resid 322...KK1 - 4801 - 480
114METMETCYSCYS(chain K and (resid 2 through 321 or (resid 322...KK1 - 4801 - 480
121LEULEUMETMET(chain L and (resid 2 through 321 or (resid 322...LL2 - 3212 - 321
122ARGARGARGARG(chain L and (resid 2 through 321 or (resid 322...LL322 - 323322 - 323
123METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
124METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
125METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
126METMETCYSCYS(chain L and (resid 2 through 321 or (resid 322...LL1 - 4801 - 480
131LEULEUMETMET(chain M and (resid 2 through 321 or (resid 322...MM2 - 3212 - 321
132ARGARGARGARG(chain M and (resid 2 through 321 or (resid 322...MM322 - 323322 - 323
133METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
134METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
135METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
136METMETCYSCYS(chain M and (resid 2 through 321 or (resid 322...MM1 - 4801 - 480
141LEULEUMETMET(chain N and (resid 2 through 321 or (resid 322...NN2 - 3212 - 321
142ARGARGARGARG(chain N and (resid 2 through 321 or (resid 322...NN322 - 323322 - 323
143METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
144METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
145METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
146METMETCYSCYS(chain N and (resid 2 through 321 or (resid 322...NN1 - 4801 - 480
151LEULEUMETMET(chain O and (resid 2 through 321 or (resid 322...OO2 - 3212 - 321
152ARGARGARGARG(chain O and (resid 2 through 321 or (resid 322...OO322 - 323322 - 323
153METMETCYSCYS(chain O and (resid 2 through 321 or (resid 322...OO1 - 4801 - 480
154METMETCYSCYS(chain O and (resid 2 through 321 or (resid 322...OO1 - 4801 - 480
161LEULEUMETMET(chain P and (resid 2 through 321 or (resid 322...PP2 - 3212 - 321
162ARGARGARGARG(chain P and (resid 2 through 321 or (resid 322...PP322 - 323322 - 323
163METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
164METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
165METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
166METMETCYSCYS(chain P and (resid 2 through 321 or (resid 322...PP1 - 4801 - 480
171LEULEUMETMET(chain Q and (resid 2 through 321 or (resid 322...QQ2 - 3212 - 321
172ARGARGARGARG(chain Q and (resid 2 through 321 or (resid 322...QQ322 - 323322 - 323
173METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
174METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
175METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
176METMETCYSCYS(chain Q and (resid 2 through 321 or (resid 322...QQ1 - 4801 - 480
181LEULEUMETMET(chain R and (resid 2 through 321 or (resid 322...RR2 - 3212 - 321
182ARGARGARGARG(chain R and (resid 2 through 321 or (resid 322...RR322 - 323322 - 323
183METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480
184METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480
185METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480
186METMETCYSCYS(chain R and (resid 2 through 321 or (resid 322...RR1 - 4801 - 480

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要素

#1: タンパク質
Glucosylglycerol phosphorylase / GGoP / 2-O-alpha-D-glucopyranosylglycerol:phosphate alpha-D-glucosyltransferase / 2-O-alpha-D- ...GGoP / 2-O-alpha-D-glucopyranosylglycerol:phosphate alpha-D-glucosyltransferase / 2-O-alpha-D-glucosylglycerol phosphorylase (retaining)


分子量: 54882.793 Da / 分子数: 18 / 由来タイプ: 組換発現
由来: (組換発現) Marinobacter adhaerens (バクテリア)
株: DSM 23420 / HP15 / 遺伝子: gtfA, HP15_2853 / プラスミド: pET-28a / 発現宿主: Escherichia coli BL21(DE3) (大腸菌)
参照: UniProt: E4PMA5, glucosylglycerol phosphorylase (configuration-retaining)
#2: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1708 / 由来タイプ: 天然 / 式: H2O

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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: 2.42 Å3/Da / 溶媒含有率: 49.15 %
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: PEG8000, MgAc

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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: SSRF / ビームライン: BL18U1 / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 6M / 検出器: PIXEL / 日付: 2022年1月1日
放射モノクロメーター: GRAPHITE / 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: 2.4→33.4 Å / Num. obs: 363096 / % possible obs: 99.6 % / 冗長度: 6.776 % / Biso Wilson estimate: 43.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.118 / Rrim(I) all: 0.128 / Χ2: 0.895 / Net I/σ(I): 12.73 / Num. measured all: 4861714
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.4-2.556.7930.7892.127762341163831142650.8040.85498.2
2.55-2.726.9030.5263.317535731092821091660.9090.56999.9
2.72-2.947.0710.3645.047196161019331017750.950.39299.8
2.94-3.226.8260.2327.9563880793723935820.9770.25199.8
3.22-3.66.7790.13414.0757385584753846470.9910.14699.9
3.6-4.156.6920.08821.8350002474862747250.9950.09699.8
4.15-5.086.2560.06329.2439454763184630690.9960.06999.8
5.08-7.146.6890.05731.1932768249031489850.9970.06199.9
7.14-33.46.4970.03839.6317737627493273010.9990.04199.3

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解析

ソフトウェア
名称バージョン分類
PHENIX1.20.1_4487精密化
XSCALEデータスケーリング
PDB_EXTRACT3.27データ抽出
XDSデータ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 6S9V

6s9v


解像度: 2.4→33.4 Å / SU ML: 0.32 / 交差検証法: THROUGHOUT / σ(F): 0.56 / 位相誤差: 25.61 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2375 35798 4.99 %
Rwork0.1939 344959 -
obs0.1961 363085 99.85 %
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: 122.48 Å2 / Biso mean: 49.2491 Å2 / Biso min: 19.77 Å2
精密化ステップサイクル: final / 解像度: 2.4→33.4 Å
タンパク質核酸リガンド溶媒全体
原子数69488 0 0 1708 71196
Biso mean---43.98 -
残基数----8638
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A26154X-RAY DIFFRACTION8.048TORSIONAL
12B26154X-RAY DIFFRACTION8.048TORSIONAL
13C26154X-RAY DIFFRACTION8.048TORSIONAL
14D26154X-RAY DIFFRACTION8.048TORSIONAL
15E26154X-RAY DIFFRACTION8.048TORSIONAL
16F26154X-RAY DIFFRACTION8.048TORSIONAL
17G26154X-RAY DIFFRACTION8.048TORSIONAL
18H26154X-RAY DIFFRACTION8.048TORSIONAL
19I26154X-RAY DIFFRACTION8.048TORSIONAL
110J26154X-RAY DIFFRACTION8.048TORSIONAL
111K26154X-RAY DIFFRACTION8.048TORSIONAL
112L26154X-RAY DIFFRACTION8.048TORSIONAL
113M26154X-RAY DIFFRACTION8.048TORSIONAL
114N26154X-RAY DIFFRACTION8.048TORSIONAL
115O26154X-RAY DIFFRACTION8.048TORSIONAL
116P26154X-RAY DIFFRACTION8.048TORSIONAL
117Q26154X-RAY DIFFRACTION8.048TORSIONAL
118R26154X-RAY DIFFRACTION8.048TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.490.325817920.272339703576299
2.49-2.590.299217980.2493438336181100
2.59-2.710.296418000.24083453936339100
2.71-2.850.296918250.23763449136316100
2.85-3.030.302618110.23773445136262100
3.03-3.260.29318080.23513450536313100
3.26-3.590.251518130.20753451336326100
3.59-4.110.223118310.18213458836419100
4.11-5.170.181318060.14973463536441100
5.17-33.40.188618420.15643488436726100

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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

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