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基本情報

登録情報
データベース: PDB / ID: 5im4
タイトルCrystal structure of designed two-component self-assembling icosahedral cage I52-32
要素
  • 6,7-dimethyl-8-ribityllumazine synthase
  • Phosphotransferase system, mannose/fructose-specific component IIA
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


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane / cytoplasm
類似検索 - 分子機能
: / PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Lumazine/riboflavin synthase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
類似検索 - ドメイン・相同性
: / Phosphotransferase system, mannose/fructose-specific component IIA
類似検索 - 構成要素
生物種Candida albicans P37005 (酵母)
Caldanaerobacter subterraneus subsp. tengcongensis (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: 3.5 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 1.22017年11月1日Group: Author supporting evidence / Database references / Derived calculations
カテゴリ: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
改定 1.32023年9月27日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA


分子量 (理論値)分子数
合計 (水以外)665,30240
ポリマ－665,30240
非ポリマー00
水00
1
A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA

A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA

A: 6,7-dimethyl-8-ribityllumazine synthase
E: 6,7-dimethyl-8-ribityllumazine synthase
C: 6,7-dimethyl-8-ribityllumazine synthase
B: 6,7-dimethyl-8-ribityllumazine synthase
D: 6,7-dimethyl-8-ribityllumazine synthase
F: Phosphotransferase system, mannose/fructose-specific component IIA
H: Phosphotransferase system, mannose/fructose-specific component IIA
G: Phosphotransferase system, mannose/fructose-specific component IIA
I: Phosphotransferase system, mannose/fructose-specific component IIA
J: Phosphotransferase system, mannose/fructose-specific component IIA
K: 6,7-dimethyl-8-ribityllumazine synthase
L: 6,7-dimethyl-8-ribityllumazine synthase
N: 6,7-dimethyl-8-ribityllumazine synthase
M: 6,7-dimethyl-8-ribityllumazine synthase
O: 6,7-dimethyl-8-ribityllumazine synthase
P: Phosphotransferase system, mannose/fructose-specific component IIA
Q: Phosphotransferase system, mannose/fructose-specific component IIA
S: Phosphotransferase system, mannose/fructose-specific component IIA
R: Phosphotransferase system, mannose/fructose-specific component IIA
T: Phosphotransferase system, mannose/fructose-specific component IIA
U: 6,7-dimethyl-8-ribityllumazine synthase
V: 6,7-dimethyl-8-ribityllumazine synthase
X: 6,7-dimethyl-8-ribityllumazine synthase
W: 6,7-dimethyl-8-ribityllumazine synthase
Y: 6,7-dimethyl-8-ribityllumazine synthase
b: Phosphotransferase system, mannose/fructose-specific component IIA
d: Phosphotransferase system, mannose/fructose-specific component IIA
c: Phosphotransferase system, mannose/fructose-specific component IIA
Z: Phosphotransferase system, mannose/fructose-specific component IIA
a: Phosphotransferase system, mannose/fructose-specific component IIA
e: 6,7-dimethyl-8-ribityllumazine synthase
f: 6,7-dimethyl-8-ribityllumazine synthase
h: 6,7-dimethyl-8-ribityllumazine synthase
g: 6,7-dimethyl-8-ribityllumazine synthase
i: 6,7-dimethyl-8-ribityllumazine synthase
j: Phosphotransferase system, mannose/fructose-specific component IIA
k: Phosphotransferase system, mannose/fructose-specific component IIA
m: Phosphotransferase system, mannose/fructose-specific component IIA
l: Phosphotransferase system, mannose/fructose-specific component IIA
n: Phosphotransferase system, mannose/fructose-specific component IIA


分子量 (理論値)分子数
合計 (水以外)1,995,905120
ポリマ－1,995,905120
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_455-y-1,x-y,z1
crystal symmetry operation3_445-x+y-1,-x-1,z1
Buried area277030 Å2
ΔGint-2400 kcal/mol
Surface area633010 Å2
手法PISA
単位格子
Length a, b, c (Å)258.820, 258.820, 641.730
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
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 A
21chain B
31chain C
41chain D
51chain E
61chain K
71chain L
81chain M
91chain N
101chain O
111chain U
121chain V
131chain W
141chain X
151chain Y
161chain e
171chain f
181chain g
191chain h
201chain i
12chain F
22chain G
32chain H
42chain I
52chain J
62chain P
72chain Q
82chain R
92chain S
102chain T
112chain Z
122chain a
132chain b
142chain c
152chain d
162chain j
172chain k
182chain l
192chain m
202chain n

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
11METMETHISHISchain AAA11 - 1671 - 157
21METMETHISHISchain BBD11 - 1671 - 157
31METMETHISHISchain CCC11 - 1671 - 157
41LYSLYSLEULEUchain DDE12 - 1652 - 155
51METMETLEULEUchain EEB11 - 1651 - 155
61METMETLEULEUchain KKK11 - 1651 - 155
71METMETGLUGLUchain LLL11 - 1661 - 156
81LYSLYSHISHISchain MMN12 - 1672 - 157
91TYRTYRLEULEUchain NNM13 - 1653 - 155
101METMETLEULEUchain OOO11 - 1651 - 155
111METMETLEULEUchain UUU11 - 1651 - 155
121METMETLEULEUchain VVV11 - 1651 - 155
131TYRTYRLEULEUchain WWX13 - 1653 - 155
141LYSLYSLEULEUchain XXW12 - 1652 - 155
151METMETLEULEUchain YYY11 - 1651 - 155
161METMETLEULEUchain eeEA11 - 1651 - 155
171METMETLEULEUchain ffFA11 - 1651 - 155
181METMETLEULEUchain ggHA11 - 1651 - 155
191METMETLEULEUchain hhGA11 - 1651 - 155
201TYRTYRGLUGLUchain iiIA13 - 1663 - 156
12METMETLYSLYSchain FFF1 - 1313 - 133
22METMETLYSLYSchain GGH1 - 1313 - 133
32METMETLYSLYSchain HHG1 - 1313 - 133
42METMETLYSLYSchain III1 - 1313 - 133
52METMETLYSLYSchain JJJ1 - 1313 - 133
62METMETLYSLYSchain PPP1 - 1313 - 133
72METMETLYSLYSchain QQQ1 - 1313 - 133
82METMETLYSLYSchain RRS1 - 1313 - 133
92METMETLYSLYSchain SSR1 - 1313 - 133
102METMETLYSLYSchain TTT1 - 1313 - 133
112METMETLYSLYSchain ZZCA1 - 1313 - 133
122METMETLYSLYSchain aaDA1 - 1313 - 133
132METMETLYSLYSchain bbZ1 - 1313 - 133
142METMETLYSLYSchain ccBA1 - 1313 - 133
152METMETLYSLYSchain ddAA1 - 1313 - 133
162METMETLYSLYSchain jjJA1 - 1313 - 133
172METMETLYSLYSchain kkKA1 - 1313 - 133
182METMETLYSLYSchain llMA1 - 1313 - 133
192METMETLYSLYSchain mmLA1 - 1313 - 133
202METMETLYSLYSchain nnNA1 - 1313 - 133

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
6,7-dimethyl-8-ribityllumazine synthase / DMRL synthase


分子量: 18101.053 Da / 分子数: 20
断片: 6,7-dimethyl-8-ribityllumazine synthase residues 12-164
変異: R29L, K30E, D33A, V40I, E50A / 由来タイプ: 組換発現 / 由来: (組換発現) Candida albicans P37005 (酵母) / 遺伝子: MEU_00538 / プラスミド: pET28b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3)
参照: UniProt: A0A0A3CUI3, 6,7-dimethyl-8-ribityllumazine synthase
#2: タンパク質
Phosphotransferase system, mannose/fructose-specific component IIA


分子量: 15164.035 Da / 分子数: 20
断片: Phosphotransferase system, mannose/fructose-specifc component IIA
変異: V45K, R47A, E51M, K52R, K55I, E56A, Q59A, S81E, E85T, Y86F
由来タイプ: 組換発現
由来: (組換発現) Caldanaerobacter subterraneus subsp. tengcongensis (strain DSM 15242 / JCM 11007 / NBRC 100824 / MB4) (バクテリア)
株: DSM 15242 / JCM 11007 / NBRC 100824 / MB4 / 遺伝子: ManX, TTE0192 / プラスミド: pET28b / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: Q8RD55

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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: 6.22 Å3/Da / 溶媒含有率: 80.22 %
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: 8 / 詳細: 0.17 M potassium sodium tartrate tetrahydrate

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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: 0.9792 Å
検出器タイプ: DECTRIS PILATUS 6M-F / 検出器: PIXEL / 日付: 2015年7月18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: 0.9792 Å / 相対比: 1
反射解像度: 3.5→213.9 Å / Num. obs: 200420 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / 冗長度: 3.6 % / Biso Wilson estimate: 104.79 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.31
反射 シェル
解像度 (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.5-3.590.6741.9197.5
3.59-3.690.5032.54199.5
3.69-3.80.4272.97199.7
3.8-3.910.3343.69199.7
3.91-4.040.2764.26199.2
4.04-4.180.2085.25198.3
4.18-4.340.1826.41199.8
4.34-4.520.157.56199.6
4.52-4.720.1288.66199.5
4.72-4.950.1258.67199.5
4.95-5.220.1218.72199.4
5.22-5.530.1148.83197.7
5.53-5.910.129.17199.8
5.91-6.390.1228.85199.8
6.39-70.10210.63199.5
7-7.820.08312.37198.8
7.82-9.030.06715.96197.6
9.03-11.070.06318.69199.5
11.07-15.650.06117.37198.7
15.65-213.90.05918.96196.5

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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
Rotation7.84 Å84.85 Å
Translation7.84 Å84.85 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 2jfb and 3lfh, but with differences

2jfb

3lfh


解像度: 3.5→110.724 Å / SU ML: 0.46 / 交差検証法: FREE R-VALUE / σ(F): 1.93 / 位相誤差: 24.59
Rfactor反射数%反射
Rfree0.2334 20026 10 %
Rwork0.2269 --
obs0.2275 200301 99.05 %
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: 267.6 Å2 / Biso mean: 103.0777 Å2 / Biso min: 39.53 Å2
精密化ステップサイクル: final / 解像度: 3.5→110.724 Å
タンパク質核酸リガンド溶媒全体
原子数40538 0 0 0 40538
残基数----5302
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00841060
X-RAY DIFFRACTIONf_angle_d1.07155299
X-RAY DIFFRACTIONf_chiral_restr0.0686734
X-RAY DIFFRACTIONf_plane_restr0.0036845
X-RAY DIFFRACTIONf_dihedral_angle_d13.23715193
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A12541X-RAY DIFFRACTION7.85TORSIONAL
12B12541X-RAY DIFFRACTION7.85TORSIONAL
13C12541X-RAY DIFFRACTION7.85TORSIONAL
14D12541X-RAY DIFFRACTION7.85TORSIONAL
15E12541X-RAY DIFFRACTION7.85TORSIONAL
16K12541X-RAY DIFFRACTION7.85TORSIONAL
17L12541X-RAY DIFFRACTION7.85TORSIONAL
18M12541X-RAY DIFFRACTION7.85TORSIONAL
19N12541X-RAY DIFFRACTION7.85TORSIONAL
110O12541X-RAY DIFFRACTION7.85TORSIONAL
111U12541X-RAY DIFFRACTION7.85TORSIONAL
112V12541X-RAY DIFFRACTION7.85TORSIONAL
113W12541X-RAY DIFFRACTION7.85TORSIONAL
114X12541X-RAY DIFFRACTION7.85TORSIONAL
115Y12541X-RAY DIFFRACTION7.85TORSIONAL
116e12541X-RAY DIFFRACTION7.85TORSIONAL
117f12541X-RAY DIFFRACTION7.85TORSIONAL
118g12541X-RAY DIFFRACTION7.85TORSIONAL
119h12541X-RAY DIFFRACTION7.85TORSIONAL
120i12541X-RAY DIFFRACTION7.85TORSIONAL
21F12656X-RAY DIFFRACTION7.85TORSIONAL
22G12656X-RAY DIFFRACTION7.85TORSIONAL
23H12656X-RAY DIFFRACTION7.85TORSIONAL
24I12656X-RAY DIFFRACTION7.85TORSIONAL
25J12656X-RAY DIFFRACTION7.85TORSIONAL
26P12656X-RAY DIFFRACTION7.85TORSIONAL
27Q12656X-RAY DIFFRACTION7.85TORSIONAL
28R12656X-RAY DIFFRACTION7.85TORSIONAL
29S12656X-RAY DIFFRACTION7.85TORSIONAL
210T12656X-RAY DIFFRACTION7.85TORSIONAL
211Z12656X-RAY DIFFRACTION7.85TORSIONAL
212a12656X-RAY DIFFRACTION7.85TORSIONAL
213b12656X-RAY DIFFRACTION7.85TORSIONAL
214c12656X-RAY DIFFRACTION7.85TORSIONAL
215d12656X-RAY DIFFRACTION7.85TORSIONAL
216j12656X-RAY DIFFRACTION7.85TORSIONAL
217k12656X-RAY DIFFRACTION7.85TORSIONAL
218l12656X-RAY DIFFRACTION7.85TORSIONAL
219m12656X-RAY DIFFRACTION7.85TORSIONAL
220n12656X-RAY DIFFRACTION7.85TORSIONAL
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 (%)
3.4992-3.53890.38976370.40245738573895
3.5389-3.58060.3826680.352560136681100
3.5806-3.62430.32476820.316161346816100
3.6243-3.67010.32066600.30325941660199
3.6701-3.71840.31256760.300660886764100
3.7184-3.76940.31256680.295960136681100
3.7694-3.82320.29326690.283860236692100
3.8232-3.88030.26426730.26560516724100
3.8803-3.94090.28026750.2636080675599
3.9409-4.00550.27416690.27256022669199
4.0055-4.07460.2626630.25665967663098
4.0746-4.14870.25996600.24745935659598
4.1487-4.22850.24936750.239360756750100
4.2285-4.31480.22896730.232360596732100
4.3148-4.40860.22886710.206360436714100
4.4086-4.51120.22776660.214559866652100
4.5112-4.6240.22746760.2086088676499
4.624-4.7490.22276660.21435998666499
4.749-4.88880.22336720.20736046671899
4.8888-5.04660.23746720.226960416713100
5.0466-5.2270.23176700.22486032670299
5.227-5.43620.21646550.21895895655097
5.4362-5.68360.22096700.21696035670599
5.6836-5.98330.24016730.22960546727100
5.9833-6.35810.24796720.247160516723100
6.3581-6.8490.22996730.222260506723100
6.849-7.5380.21496670.20786003667099
7.538-8.62850.16796560.16225910656697
8.6285-10.86950.13536730.13526040671399
10.8695-110.77990.24456460.25185864651097
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)
13.9988-1.4771-0.69252.73931.12322.43120.14390.234-0.0096-0.0815-0.09180.2247-0.11720.0434-00.66920.0811-0.22820.6411-0.06590.89-165.1781-145.226874.6009
24.20451.59411.11763.22591.3732.059-0.00040.05720.0611-0.1661-0.12970.1471-0.02790.0989-00.56810.1248-0.06330.4352-0.0040.7308-159.0149-125.088190.4204
33.9116-0.8982-0.91192.44721.4392.0770.05310.13780.3892-0.2482-0.030.0986-0.0068-0.1348-00.6355-0.0391-0.00370.37190.03760.5811-133.1464-125.431694.4577
42.6114-0.198-0.25823.51792.02723.05160.1058-0.03390.0692-0.4097-0.0115-0.1706-0.1817-0.080900.63140.01410.0450.51560.01160.5226-123.3838-145.721880.6977
55.27370.38371.59122.39220.0142.9482-0.00590.3023-0.0354-0.2108-0.02160.249-0.05550.1217-00.6640.0864-0.09390.5628-0.0730.4997-143.1033-157.505568.4099
63.86-1.51492.81011.4434-1.31480.8776-0.1356-0.7465-0.33880.09310.3848-0.0024-0.1036-0.49910.00040.78880.2112-0.20711.1449-0.00210.9442-192.5244-134.851466.8719
71.86230.4901-0.42535.23150.65380.3691-0.0081-0.0097-0.24560.51170.00640.02630.19170.0930.00070.89640.2462-0.1520.5015-0.04760.9655-163.2008-96.9853100.3088
83.24363.75330.07222.43860.4210.89420.175-0.1779-0.39180.0166-0.1152-0.3608-0.07890.01310.00460.6321-0.1351-0.01250.40480.05591.0374-106.72-111.418199.1953
93.396-0.9671-2.44450.33150.89263.0705-0.5972-0.324-0.23780.13480.25380.11430.23460.261-0.0970.77930.05790.35540.6236-0.02750.7388-100.9546-158.354664.5599
100.84760.16741.98491.60311.70124.48650.1639-0.20410.10170.38460.0081-0.19730.5393-0.46640.00060.9721-0.1366-0.07891.0674-0.1420.6945-154.004-172.66444.7862
111.7796-0.93840.14984.6052-0.80472.1890.0492-0.00970.11980.0172-0.0791-0.05860.1617-0.039200.683-0.01840.03860.6504-0.01040.5462-235.2057-112.6276-6.4645
121.4503-0.55270.53054.85351.25283.4588-0.11-0.15510.1926-0.08230.08-0.43180.01760.0317-00.6318-0.0673-0.08040.68520.0010.6614-240.4916-88.88232.8913
132.021-0.59470.73693.3154-0.69765.1075-0.0309-0.08160.08990.0462-0.0805-0.1084-0.03790.437600.66980.0266-0.20110.7513-0.08230.6801-235.1324-88.973428.5814
143.5695-1.050.56134.11820.70441.3709-0.21420.06850.02710.09030.0347-0.15730.0136-0.096500.75210.145-0.12850.8449-0.0430.6796-226.7759-113.160234.8446
151.43810.09721.16862.6161.72563.8850.02430.04730.0187-0.0376-0.0047-0.30390.145-0.0326-00.74320.11410.04420.7484-0.02350.6938-227.3158-127.856413.5469
16-0.02841.6873-0.27061.1492-1.33774.96260.089-0.01690.06010.17870.15260.03970.0546-0.71960.00040.82730.12740.18471.06760.04860.5543-234.7764-105.0006-35.7501
170.22160.70070.43114.9771-2.02910.12010.0523-0.07980.0456-0.12040.15680.6134-0.10450.21260.00070.847-0.07590.04070.75040.05280.9724-241.4411-58.7698-0.3303
182.14751.12912.08381.92362.50692.12260.2319-0.28150.01280.0031-0.32180.04570.2354-0.5491-0.00070.9922-0.1478-0.19951.0283-0.14790.7724-225.7223-74.949253.5626
193.4003-2.31471.55760.1636-0.96930.98670.1157-0.1608-0.3653-0.24010.18070.2131-0.0904-0.34910.00010.89160.0994-0.34940.94940.03121.1036-209.4754-130.940351.7849
201.8568-2.5339-2.89753.21451.45271.8536-0.03450.074-0.00510.1436-0.08430.26680.0027-0.0339-00.72730.1537-0.06670.7384-0.04290.752-214.6689-149.5652-3.5311
213.5864-0.06460.88983.6676-1.34792.15020.0768-0.24220.10740.29050.0337-0.0119-0.1561-0.1054-00.5820.0923-0.0490.6035-0.06850.4784-60.7199-113.3174-86.4542
225.82070.71490.97253.5197-1.02131.8554-0.2097-0.17040.24040.02490.20130.0241-0.165-0.369-0.00010.4280.1002-0.00150.483-0.03130.5597-77.3788-100.2077-101.8125
232.86931.104-0.04724.0935-1.01041.33270.0133-0.08630.04580.0864-0.06190.11180.0737-0.258100.45440.0090.04610.76150.09470.6424-98.3037-115.35-105.6594
242.4044-0.70690.77093.1307-1.5242.67780.0568-0.2381-0.07050.27690.06720.19140.0096-0.077500.6614-0.12890.00710.75650.13510.6931-94.7075-137.6617-92.7987
252.52841.56890.94532.36491.20222.01360.2194-0.33220.02860.2118-0.04350.04090.1028-0.106300.6962-0.0267-0.03130.71150.14360.616-71.8863-136.2203-80.2802
261.1904-1.16022.87890.38160.87534.14250.27790.30750.12550.0449-0.08120.0950.30040.50730.00270.847-0.0056-0.0481.13890.29430.6276-54.0902-142.994-56.8654
272.25422.31781.73133.68752.58371.4922-0.18520.153-0.1979-0.28730.2419-0.0982-0.23590.1369-00.9129-0.0699-0.130.7989-0.10780.6182-43.3896-89.7024-78.7933
281.5423-1.8513-0.04884.077-0.9871-0.05520.3045-0.064-0.0901-0.4616-0.25120.00580.048-0.02860.00010.90280.2223-0.1350.5718-0.07720.8067-89.026-74.3784-111.6983
294.9055-0.37020.1266-0.8083-1.28791.1274-0.04340.4335-0.37840.04170.0310.0597-0.12840.15990.00090.417-0.0055-0.02280.9174-0.05371.0525-128.0269-118.0463-110.5674
300.35882.8246-1.36732.238-1.47041.7351-0.4314-0.1313-0.1637-0.3790.0845-0.16640.24510.0395-0.00290.9537-0.08290.21010.92980.27661.0997-106.3293-160.5701-76.7873
313.12491.8219-0.5562.8544-0.61871.3515-0.027-0.0985-0.24770.09320.05220.06460.06190.114-00.8503-0.0413-0.00380.65240.03360.6135-207.66646.1969-5.6169
322.88421.09311.35792.74780.09923.82910.05680.0236-0.26520.0803-0.1252-0.1228-0.03340.0341-00.8108-0.06360.10350.6417-0.03250.8184-222.9645-12.8974-15.0734
333.50762.0388-1.3691.588-1.11414.6822-0.1040.243-0.04860.0771-0.0203-0.00060.22970.017700.793-0.02130.11940.7116-0.18930.7855-218.9312-14.6479-40.9912
342.82921.55150.81954.04290.9560.8457-0.16740.1524-0.1229-0.01970.1613-0.0480.04090.1732-00.5869-0.00510.12420.817-0.10220.5683-200.20842.715-47.3064
352.41521.3310.55892.6634-0.07784.8776-0.00420.0287-0.19510.06410.1443-0.1093-0.01890.096600.6313-0.02240.01370.7124-0.02680.6328-193.29915.4437-25.407
360.0943-0.0524-0.01291.942-1.02224.911-0.0412-0.0351-0.1605-0.16360.20450.0317-0.4555-0.598300.9175-0.0169-0.03861.0420.20420.6685-210.2586-1.152123.6346
370.92831.2588-1.24595.0744-1.2865-0.11710.01730.08030.1928-0.36350.2620.3592-0.03220.0785-01.033-0.1724-0.10210.81360.08771.0083-237.0466-39.3604-11.4843
380.6185-0.2839-1.15832.15682.98062.71130.2454-0.1359-0.2916-0.4161-0.47240.0285-0.5494-0.4416-0.00291.19260.08930.11950.7396-0.22180.8244-216.0973-31.8357-65.7242
395.22570.4256-2.2893-0.4949-0.23791.90250.13560.09180.4590.27040.02580.1007-0.0513-0.3183-00.7838-0.02720.27950.8533-0.09750.8421-176.37211.0729-63.8662
403.36172.13682.9491.32380.41511.40640.0521-0.34390.0343-0.0334-0.16120.06910.0293-0.2592-00.61240.00010.04290.9821-0.09230.7487-172.850629.8686-8.6659
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA11 - 167
2X-RAY DIFFRACTION2chain BB11 - 167
3X-RAY DIFFRACTION3chain CC11 - 167
4X-RAY DIFFRACTION4chain DD12 - 165
5X-RAY DIFFRACTION5chain EE11 - 165
6X-RAY DIFFRACTION6chain FF1 - 131
7X-RAY DIFFRACTION7chain GG1 - 131
8X-RAY DIFFRACTION8chain HH1 - 131
9X-RAY DIFFRACTION9chain II1 - 131
10X-RAY DIFFRACTION10chain JJ1 - 131
11X-RAY DIFFRACTION11chain KK11 - 165
12X-RAY DIFFRACTION12chain LL11 - 166
13X-RAY DIFFRACTION13chain MM12 - 167
14X-RAY DIFFRACTION14chain NN13 - 165
15X-RAY DIFFRACTION15chain OO11 - 165
16X-RAY DIFFRACTION16chain PP1 - 131
17X-RAY DIFFRACTION17chain QQ1 - 131
18X-RAY DIFFRACTION18chain RR1 - 131
19X-RAY DIFFRACTION19chain SS1 - 131
20X-RAY DIFFRACTION20chain TT1 - 131
21X-RAY DIFFRACTION21chain UU11 - 165
22X-RAY DIFFRACTION22chain VV11 - 165
23X-RAY DIFFRACTION23chain WW13 - 165
24X-RAY DIFFRACTION24chain XX12 - 165
25X-RAY DIFFRACTION25chain YY11 - 165
26X-RAY DIFFRACTION26chain ZZ1 - 131
27X-RAY DIFFRACTION27chain aa1 - 131
28X-RAY DIFFRACTION28chain bb1 - 131
29X-RAY DIFFRACTION29chain cc1 - 131
30X-RAY DIFFRACTION30chain dd1 - 131
31X-RAY DIFFRACTION31chain ee11 - 165
32X-RAY DIFFRACTION32chain ff11 - 165
33X-RAY DIFFRACTION33chain gg11 - 165
34X-RAY DIFFRACTION34chain hh11 - 165
35X-RAY DIFFRACTION35chain ii13 - 166
36X-RAY DIFFRACTION36chain jj1 - 131
37X-RAY DIFFRACTION37chain kk1 - 131
38X-RAY DIFFRACTION38chain ll1 - 131
39X-RAY DIFFRACTION39chain mm1 - 131
40X-RAY DIFFRACTION40chain nn1 - 131

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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