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基本情報

登録情報
データベース: PDB / ID: 5im5
タイトルCrystal structure of designed two-component self-assembling icosahedral cage I53-40
要素
  • Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
  • Designed Riboflavin synthase
キーワードPROTEIN BINDING / icosahedron / designed protein cage / two-component / computational design / protein engineering / Rosetta / self-assembling / co-assembling / multimerization / symmetry / nanomaterial / nanostructure
機能・相同性
機能・相同性情報


riboflavin synthase / 2-dehydro-3-deoxy-phosphogluconate aldolase / riboflavin synthase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / riboflavin synthase complex / riboflavin biosynthetic process
類似検索 - 分子機能
Riboflavin synthase, archaeal / KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / Lumazine/riboflavin synthase / KDPG/KHG aldolase / KDPG and KHG aldolase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily ...Riboflavin synthase, archaeal / KDPG/KHG aldolase, active site 2 / KDPG and KHG aldolases Schiff-base forming residue. / KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / Lumazine/riboflavin synthase / KDPG/KHG aldolase / KDPG and KHG aldolase / Lumazine/riboflavin synthase / Lumazine/riboflavin synthase superfamily / 6,7-dimethyl-8-ribityllumazine synthase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
2-dehydro-3-deoxy-phosphogluconate aldolase / Riboflavin synthase
類似検索 - 構成要素
生物種Methanocaldococcus jannaschii (メタン生成菌)
Vibrionales bacterium (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: 3.699 Å
データ登録者Liu, Y.A. / Cascio, D. / Sawaya, M.R. / Bale, J.B. / Collazo, M.J. / Thomas, C. / Sheffler, W. / King, N.P. / Baker, D. / Yeates, T.O.
引用ジャーナル: Science / 年: 2016
タイトル: Accurate design of megadalton-scale two-component icosahedral protein complexes.
著者: Bale, J.B. / Gonen, S. / Liu, Y. / Sheffler, W. / Ellis, D. / Thomas, C. / Cascio, D. / Yeates, T.O. / Gonen, T. / King, N.P. / Baker, D.
履歴
登録2016年3月5日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年7月27日Provider: repository / タイプ: Initial release
改定 1.12016年8月10日Group: Database references
改定 1.22023年9月27日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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
K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase


分子量 (理論値)分子数
合計 (水以外)606,00230
ポリマ－606,00230
非ポリマー00
水00
1
K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase

K: Designed Riboflavin synthase
M: Designed Riboflavin synthase
O: Designed Riboflavin synthase
Q: Designed Riboflavin synthase
S: Designed Riboflavin synthase
A: Designed Riboflavin synthase
B: Designed Riboflavin synthase
C: Designed Riboflavin synthase
D: Designed Riboflavin synthase
E: Designed Riboflavin synthase
F: Designed Riboflavin synthase
G: Designed Riboflavin synthase
H: Designed Riboflavin synthase
I: Designed Riboflavin synthase
J: Designed Riboflavin synthase
P: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
T: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
N: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
V: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
W: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
U: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Y: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
Z: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
X: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
2: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
4: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
1: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
L: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
R: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
3: Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase


分子量 (理論値)分子数
合計 (水以外)2,424,006120
ポリマ－2,424,006120
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation3_757-x+2,y,-z+21
crystal symmetry operation4_567x,-y+1,-z+21
Buried area254070 Å2
ΔGint-2120 kcal/mol
Surface area766940 Å2
手法PISA
単位格子
Length a, b, c (Å)265.620, 279.810, 301.330
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
対称性点対称性: (シェーンフリース記号: I (正20面体型対称))
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11chain 1
21chain 2
31chain 3
41chain 4
51chain L
61chain N
71chain P
81chain R
91chain T
101chain U
111chain V
121chain W
131chain X
141chain Y
151chain Z
12chain A
22chain B
32chain C
42chain D
52chain E
62chain F
72chain G
82chain H
92chain I
102chain J
112chain K
122chain M
132chain O
142chain Q
152chain S

NCSドメイン領域:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERPROPROchain 11AA2 - 2092 - 209
21SERSERPROPROchain 22Y2 - 2092 - 209
31SERSERPROPROchain 33DA2 - 2092 - 209
41SERSERPROPROchain 44Z2 - 2092 - 209
51SERSERPROPROchain LLBA2 - 2092 - 209
61SERSERPROPROchain NNR2 - 2092 - 209
71SERSERPROPROchain PPP2 - 2092 - 209
81SERSERPROPROchain RRCA2 - 2092 - 209
91SERSERPROPROchain TTQ2 - 2092 - 209
101SERSERPROPROchain UUU2 - 2092 - 209
111SERSERPROPROchain VVS2 - 2092 - 209
121SERSERPROPROchain WWT2 - 2092 - 209
131SERSERPROPROchain XXX2 - 2092 - 209
141SERSERPROPROchain YYV2 - 2092 - 209
151SERSERPROPROchain ZZW2 - 2092 - 209
12THRTHRGLYGLYchain AAF2 - 1432 - 143
22THRTHRGLYGLYchain BBG2 - 1432 - 143
32THRTHRGLYGLYchain CCH2 - 1432 - 143
42THRTHRLYSLYSchain DDI2 - 1422 - 142
52THRTHRGLYGLYchain EEJ2 - 1432 - 143
62THRTHRLYSLYSchain FFK2 - 1422 - 142
72THRTHRGLYGLYchain GGL2 - 1432 - 143
82THRTHRGLYGLYchain HHM2 - 1432 - 143
92THRTHRGLYGLYchain IIN2 - 1432 - 143
102THRTHRLYSLYSchain JJO2 - 1422 - 142
112THRTHRGLYGLYchain KKA2 - 1432 - 143
122THRTHRLYSLYSchain MMB2 - 1422 - 142
132THRTHRLYSLYSchain OOC2 - 1422 - 142
142THRTHRGLYGLYchain QQD2 - 1432 - 143
152THRTHRGLYGLYchain SSE2 - 1432 - 143

NCSアンサンブル:
ID
1
2
詳細120-mer icosahedral cage according to gel filtration, transmission electron microscopy, small-angle X-ray scattering

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要素

#1: タンパク質
Designed Riboflavin synthase


分子量: 17249.373 Da / 分子数: 15 / 断片: Riboflavin synthase
変異: I20A, K23L, K24T, E27M, L28E, K109A, D112K, W113I, K116A, E120I, E124L
由来タイプ: 組換発現
由来: (組換発現) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (メタン生成菌)
株: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
遺伝子: ribC, MJ1184 / プラスミド: pET29b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q58584, riboflavin synthase
#2: タンパク質
Designed Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase


分子量: 23150.732 Da / 分子数: 15
断片: Keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase
変異: D47S, E51K, R54M, Q59S, E74V, E102I / 由来タイプ: 組換発現
由来: (組換発現) Vibrionales bacterium (strain SWAT-3) (バクテリア)
株: SWAT-3 / 遺伝子: VSWAT3_13722 / プラスミド: pET29b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: A5KUH7, 4-hydroxy-2-oxoglutarate aldolase

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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: 4.64 Å3/Da / 溶媒含有率: 73.47 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 4.6
詳細: 100 mM sodium acetate pH 4.6, 0.4 M calcium chloride, 3.2% (v/v) isoproponal

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データ収集

回折平均測定温度: 100 K
放射光源由来: シンクロトロン / サイト: APS / ビームライン: 24-ID-C / 波長: 0.9791 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2014年10月16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: 0.9791 Å / 相対比: 1
反射解像度: 3.699→199.3 Å / Num. obs: 118064 / % possible obs: 99 % / Observed criterion σ(I): -3 / 冗長度: 4.2 % / Biso Wilson estimate: 70.7 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.168 / Net I/σ(I): 8.34
反射 シェル
解像度 (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.7-3.80.8441.84195.1
3.8-3.90.6912.56199.7
3.9-4.010.5443.24199.7
4.01-4.140.3954.36199.8
4.14-4.270.3175.35199.7
4.27-4.420.2676.12199.7
4.42-4.590.2426.5199.6
4.59-4.780.2037.43198.8
4.78-4.990.1787.9197.9
4.99-5.230.1987.59199.6
5.23-5.510.2127.23199.9
5.51-5.850.2047.31199.8
5.85-6.250.187.99199.7
6.25-6.750.1658.41199.1
6.75-7.40.10312.01197.5
7.4-8.270.06318.74199.4
8.27-9.550.04525.61199.4
9.55-11.70.0427.83198.7
11.7-16.540.04124.69196.5

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位相決定

位相決定手法: 分子置換
Phasing MRModel details: Phaser MODE: MR_AUTO
最高解像度最低解像度
Rotation8.54 Å96.35 Å
Translation8.54 Å96.35 Å

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解析

ソフトウェア
名称バージョン分類
XSCALEデータスケーリング
PHASER2.5.6位相決定
PHENIX精密化
PDB_EXTRACT3.2データ抽出
XDSデータ削減
精密化構造決定の手法: 分子置換
開始モデル: Rosetta design generated based on the PDB files 2b98 and 4e38, but with differences

2b98

4e38


解像度: 3.699→199.257 Å / SU ML: 0.46 / 交差検証法: FREE R-VALUE / σ(F): 1.35 / 位相誤差: 25.32
Rfactor反射数%反射
Rfree0.2468 11798 10 %
Rwork0.24 --
obs0.2407 118004 98.92 %
溶媒の処理減衰半径: 0.8 Å / VDWプローブ半径: 1.1 Å
原子変位パラメータBiso max: 163.61 Å2 / Biso mean: 99.5539 Å2 / Biso min: 64.28 Å2
精密化ステップサイクル: final / 解像度: 3.699→199.257 Å
タンパク質核酸リガンド溶媒全体
原子数39198 0 0 0 39198
残基数----5245
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01139768
X-RAY DIFFRACTIONf_angle_d1.34753922
X-RAY DIFFRACTIONf_chiral_restr0.0846555
X-RAY DIFFRACTIONf_plane_restr0.0086894
X-RAY DIFFRACTIONf_dihedral_angle_d14.43614899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11114623X-RAY DIFFRACTION9.021TORSIONAL
12214623X-RAY DIFFRACTION9.021TORSIONAL
13314623X-RAY DIFFRACTION9.021TORSIONAL
14414623X-RAY DIFFRACTION9.021TORSIONAL
15L14623X-RAY DIFFRACTION9.021TORSIONAL
16N14623X-RAY DIFFRACTION9.021TORSIONAL
17P14623X-RAY DIFFRACTION9.021TORSIONAL
18R14623X-RAY DIFFRACTION9.021TORSIONAL
19T14623X-RAY DIFFRACTION9.021TORSIONAL
110U14623X-RAY DIFFRACTION9.021TORSIONAL
111V14623X-RAY DIFFRACTION9.021TORSIONAL
112W14623X-RAY DIFFRACTION9.021TORSIONAL
113X14623X-RAY DIFFRACTION9.021TORSIONAL
114Y14623X-RAY DIFFRACTION9.021TORSIONAL
115Z14623X-RAY DIFFRACTION9.021TORSIONAL
21A10299X-RAY DIFFRACTION9.021TORSIONAL
22B10299X-RAY DIFFRACTION9.021TORSIONAL
23C10299X-RAY DIFFRACTION9.021TORSIONAL
24D10299X-RAY DIFFRACTION9.021TORSIONAL
25E10299X-RAY DIFFRACTION9.021TORSIONAL
26F10299X-RAY DIFFRACTION9.021TORSIONAL
27G10299X-RAY DIFFRACTION9.021TORSIONAL
28H10299X-RAY DIFFRACTION9.021TORSIONAL
29I10299X-RAY DIFFRACTION9.021TORSIONAL
210J10299X-RAY DIFFRACTION9.021TORSIONAL
211K10299X-RAY DIFFRACTION9.021TORSIONAL
212M10299X-RAY DIFFRACTION9.021TORSIONAL
213O10299X-RAY DIFFRACTION9.021TORSIONAL
214Q10299X-RAY DIFFRACTION9.021TORSIONAL
215S10299X-RAY DIFFRACTION9.021TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.6991-3.74110.37483560.38513204356091
3.7411-3.78510.34333910.33883516390799
3.7851-3.83130.36623920.33813524391699
3.8313-3.87980.32663930.312935373930100
3.8798-3.93090.34023900.320735213911100
3.9309-3.98470.28163920.300935313923100
3.9847-4.04160.30973960.283935643960100
4.0416-4.1020.2763930.277435393932100
4.102-4.16610.2783920.283335283920100
4.1661-4.23440.27573990.2635853984100
4.2344-4.30740.23583930.23635433936100
4.3074-4.38570.24343950.235935463941100
4.3857-4.47010.25443900.242235143904100
4.4701-4.56130.24563930.235335413934100
4.5613-4.66050.23833950.234435483943100
4.6605-4.7690.22363900.22033512390298
4.769-4.88820.25173870.22663483387098
4.8882-5.02040.24723900.22533510390098
5.0204-5.16810.23163940.24135463940100
5.1681-5.3350.27283990.25535923991100
5.335-5.52570.29033960.269235573953100
5.5257-5.74690.29273960.268335773973100
5.7469-6.00850.30823950.27935583953100
6.0085-6.32530.26743990.266135923991100
6.3253-6.72160.25833950.27723552394799
6.7216-7.24060.22673910.22633522391398
7.2406-7.96930.19993960.19743561395799
7.9693-9.12240.13624040.140236374041100
9.1224-11.49320.14994010.14323604400598
11.4932-199.54660.26884050.25883662406796
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)
14.6993-1.0817-0.38534.5020.15025.5018-0.07070.1533-0.5035-0.27590.03630.170.3234-0.23120.04230.5019-0.0118-0.0380.8260.01910.7864287.563473.078261.656
23.7112-1.35190.01537.3126-2.14214.199-0.09740.4998-0.0513-0.39690.1265-0.00560.41810.0757-0.02510.6087-0.065-0.04760.81660.02530.6151271.357562.6049278.4123
35.06920.5643-0.01724.46370.30165.09850.1318-0.0249-0.5025-0.1686-0.14740.13050.31650.1530.00670.6196-0.0181-0.1240.88020.01130.789249.096281.1717248.9831
45.04980.5421-0.89135.9052-0.54994.2773-0.13480.0631-0.3731-0.2055-0.13920.13570.4216-0.07640.27440.6597-0.09910.00190.93410.04290.8214247.557167.5879270.5584
54.3779-0.61360.01963.7835-0.94156.5593-0.0730.0462-0.2113-0.29080.0482-0.0270.5389-0.0740.03550.5149-0.076-0.00120.6366-0.01060.634273.756584.5395243.4233
64.34870.57121.89686.2421.62255.69220.01110.40140.0906-0.08120.0847-0.296-0.07780.2279-0.08550.47550.0411-0.04580.5485-0.03090.7075288.3737134.6161224.4305
73.03520.27410.75864.5776-1.44446.43620.13070.22240.0391-0.2124-0.0159-0.21580.07580.2526-0.09650.75370.0559-0.03820.5842-0.01350.939296.321158.3715229.1469
86.40940.880.73325.234-0.31494.4849-0.02870.3238-0.004-0.2671-0.13570.04360.07790.44880.18310.7070.1304-0.0960.6029-0.030.8112323.5698132.2056246.0153
96.80972.45580.21955.0314-2.35254.70330.06910.3485-0.171-0.18130.0871-0.0505-0.2250.2457-0.12770.6755-0.0202-0.03590.5663-0.12170.7794318.0667156.9371242.562
105.6398-0.7753-0.15216.49851.34395.3777-0.03390.31240.2963-0.3479-0.0862-0.0972-0.14530.17020.11890.66780.0664-0.00950.403-0.02620.7125305.1123118.4001234.8455
116.76570.5924-2.14395.5445-1.98765.5218-0.0604-0.3727-0.2181-0.0596-0.0534-0.64350.46970.31480.07770.7487-0.0184-0.05380.5352-0.0810.5943342.7099116.9734295.7866
123.0707-0.557-0.65376.213-0.55522.80150.0858-0.2148-0.38730.2726-0.04030.62460.0541-0.5961-0.05920.48820.0429-0.04850.8382-0.04310.7504192.076184.8324363.2576
135.85631.77991.11134.07230.17075.6484-0.0772-0.1245-0.31150.03720.1937-0.44010.33460.3889-0.11030.81070.0347-0.07010.6855-0.06560.5654337.8416109.0665319.5954
146.45520.1997-1.02082.5491-0.31412.7766-0.1306-0.1949-0.94020.02680.1322-0.02640.6809-0.0921-0.01730.79320.1407-0.05050.63070.03930.76319.691163.1799251.7146
153.58130.50560.00455.9008-0.55864.3630.19590.1886-0.48460.1258-0.1816-0.2937-0.10260.1364-0.0340.81120.0169-0.07030.6432-0.05980.6488320.977481.8805293.4928
165.4037-0.62891.96631.90150.85525.7590.05820.02980.01860.06110.0439-0.2381-0.20780.2949-0.11210.672-0.02140.08830.6081-0.05210.6674342.310890.9091247.5482
175.27430.4554-0.92156.6061-1.38467.4023-0.2586-0.0788-0.3154-0.16930.1475-0.11670.01880.55010.09780.71050.0519-0.02990.61430.03660.5156324.332687.4413318.1644
183.652-1.37221.42653.39760.19325.56930.06880.06730.1392-0.45780.0337-0.1026-0.2184-0.2744-0.10.7501-0.01420.11990.6381-0.03310.6455204.421213.8158345.6677
194.42510.0667-0.54745.86830.33048.40260.2120.0639-0.21290.125-0.0354-0.36790.23070.5014-0.17120.6390.0304-0.01370.6457-0.03450.4877332.215100.1803279.7054
202.6338-0.9644-0.26425.3937-1.46195.70640.05670.3527-0.1122-0.3749-0.15750.16560.1371-0.02970.07860.5190.0816-0.06030.5492-0.15540.6983314.873186.3828224.6014
212.15630.7448-0.68423.9772-1.55743.6040.0244-0.1708-0.03270.2101-0.1213-0.65730.10340.85240.11740.734-0.0617-0.05311.173-0.05470.9637370.0489134.8659282.9644
220.9357-0.5925-0.54925.1710.93182.81650.11890.23210.1703-0.321-0.1183-0.603-0.51840.33270.00240.8508-0.07760.15861.00970.03590.7959360.8071159.9868258.8292
234.25930.48391.2332.35760.30524.7365-0.01860.3114-0.4396-0.38290.0013-0.19530.17950.53570.03290.7020.18680.05820.7742-0.10.903357.5685124.9968250.6351
242.5358-0.6247-0.8652.1830.04365.4596-0.0618-0.376-0.36040.21480.1125-0.16240.50430.1692-0.0360.77660.1793-0.08930.84010.04611.0052308.024644.6284321.4675
252.93521.2997-0.16572.33020.51432.2498-0.11590.1696-0.5728-0.29830.0759-0.33710.33420.34230.01811.06480.13210.0440.7292-0.14980.9827316.363147.7146286.5538
263.9595-0.17571.28621.01250.20164.77130.02810.0372-0.70660.09980.00110.12490.7452-0.1844-0.03250.9574-0.08070.04650.60210.09141.027284.022435.1924296.3248
274.27752.01020.87823.63670.18082.7855-0.14680.62340.3157-0.73030.1253-0.01-0.1318-0.11980.01460.97180.1163-0.09290.81690.02640.6964270.7024121.6569197.0133
284.6806-1.0869-0.75683.61950.89253.09220.08140.3743-0.2877-0.2430.02840.38840.3076-0.2759-0.09440.8947-0.0906-0.07840.6493-0.12060.8628245.806697.2386206.2331
294.47590.6934-0.0972.60890.96323.1453-0.0738-0.17880.14950.24620.1789-0.03650.11260.1936-0.10350.70190.15930.0860.76970.01560.6529221.6263201.7227374.9783
302.6358-0.3819-0.05224.0365-1.50893.88190.14410.2252-0.4517-0.5462-0.1342-0.20280.35880.2020.00140.71510.06930.06910.8431-0.12820.7318280.778889.2954209.4245
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA2 - 143
2X-RAY DIFFRACTION2chain BB2 - 143
3X-RAY DIFFRACTION3chain CC2 - 143
4X-RAY DIFFRACTION4chain DD2 - 142
5X-RAY DIFFRACTION5chain EE2 - 143
6X-RAY DIFFRACTION6chain FF2 - 142
7X-RAY DIFFRACTION7chain GG2 - 143
8X-RAY DIFFRACTION8chain HH2 - 143
9X-RAY DIFFRACTION9chain II2 - 143
10X-RAY DIFFRACTION10chain JJ2 - 142
11X-RAY DIFFRACTION11chain KK2 - 143
12X-RAY DIFFRACTION12chain LL2 - 209
13X-RAY DIFFRACTION13chain MM2 - 142
14X-RAY DIFFRACTION14chain NN2 - 209
15X-RAY DIFFRACTION15chain OO2 - 142
16X-RAY DIFFRACTION16chain PP2 - 209
17X-RAY DIFFRACTION17chain QQ2 - 143
18X-RAY DIFFRACTION18chain RR2 - 209
19X-RAY DIFFRACTION19chain SS2 - 143
20X-RAY DIFFRACTION20chain TT2 - 209
21X-RAY DIFFRACTION21chain UU2 - 209
22X-RAY DIFFRACTION22chain VV2 - 209
23X-RAY DIFFRACTION23chain WW2 - 209
24X-RAY DIFFRACTION24chain XX2 - 209
25X-RAY DIFFRACTION25chain YY2 - 209
26X-RAY DIFFRACTION26chain ZZ2 - 209
27X-RAY DIFFRACTION27chain 112 - 209
28X-RAY DIFFRACTION28chain 222 - 209
29X-RAY DIFFRACTION29chain 332 - 209
30X-RAY DIFFRACTION30chain 442 - 209

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万見について

-
お知らせ

-
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

-
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

+
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

+
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