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- PDB-5im6: Crystal structure of designed two-component self-assembling icosa... -

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基本情報

登録情報
データベース: PDB / ID: 5im6
タイトルCrystal structure of designed two-component self-assembling icosahedral cage I32-28
要素
  • Designed self-assembling icosahedral cage I32-28 dimeric subunit
  • Designed self-assembling icosahedral cage I32-28 trimeric subunit
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


corrinoid adenosyltransferase activity / 転移酵素; メチル基以外のアルキル基またはアリル基を移すもの; - / cobalamin biosynthetic process / ATP binding / metal ion binding
類似検索 - 分子機能
Protein of unknown function DUF3809 / Protein of unknown function (DUF3809) / Cobalamin adenosyltransferase-like / Corrinoid adenosyltransferase, PduO-type / Cobalamin adenosyltransferase / Cobalamin adenosyltransferase-like superfamily
類似検索 - ドメイン・相同性
Cobalamin adenosyltransferase / DUF3809 domain-containing protein
類似検索 - 構成要素
生物種Burkholderia thailandensis E264 (バクテリア)
Deinococcus radiodurans R1 (放射線耐性)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 5.588 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Designed self-assembling icosahedral cage I32-28 trimeric subunit
B: Designed self-assembling icosahedral cage I32-28 trimeric subunit
C: Designed self-assembling icosahedral cage I32-28 trimeric subunit
D: Designed self-assembling icosahedral cage I32-28 trimeric subunit
E: Designed self-assembling icosahedral cage I32-28 trimeric subunit
F: Designed self-assembling icosahedral cage I32-28 trimeric subunit
G: Designed self-assembling icosahedral cage I32-28 trimeric subunit
H: Designed self-assembling icosahedral cage I32-28 trimeric subunit
I: Designed self-assembling icosahedral cage I32-28 trimeric subunit
J: Designed self-assembling icosahedral cage I32-28 trimeric subunit
U: Designed self-assembling icosahedral cage I32-28 dimeric subunit
V: Designed self-assembling icosahedral cage I32-28 dimeric subunit
W: Designed self-assembling icosahedral cage I32-28 dimeric subunit
X: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Y: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Z: Designed self-assembling icosahedral cage I32-28 dimeric subunit
a: Designed self-assembling icosahedral cage I32-28 dimeric subunit
b: Designed self-assembling icosahedral cage I32-28 dimeric subunit
c: Designed self-assembling icosahedral cage I32-28 dimeric subunit
d: Designed self-assembling icosahedral cage I32-28 dimeric subunit
K: Designed self-assembling icosahedral cage I32-28 trimeric subunit
L: Designed self-assembling icosahedral cage I32-28 trimeric subunit
M: Designed self-assembling icosahedral cage I32-28 trimeric subunit
N: Designed self-assembling icosahedral cage I32-28 trimeric subunit
O: Designed self-assembling icosahedral cage I32-28 trimeric subunit
P: Designed self-assembling icosahedral cage I32-28 trimeric subunit
Q: Designed self-assembling icosahedral cage I32-28 trimeric subunit
R: Designed self-assembling icosahedral cage I32-28 trimeric subunit
S: Designed self-assembling icosahedral cage I32-28 trimeric subunit
T: Designed self-assembling icosahedral cage I32-28 trimeric subunit
e: Designed self-assembling icosahedral cage I32-28 dimeric subunit
f: Designed self-assembling icosahedral cage I32-28 dimeric subunit
g: Designed self-assembling icosahedral cage I32-28 dimeric subunit
h: Designed self-assembling icosahedral cage I32-28 dimeric subunit
i: Designed self-assembling icosahedral cage I32-28 dimeric subunit
j: Designed self-assembling icosahedral cage I32-28 dimeric subunit
k: Designed self-assembling icosahedral cage I32-28 dimeric subunit
l: Designed self-assembling icosahedral cage I32-28 dimeric subunit
m: Designed self-assembling icosahedral cage I32-28 dimeric subunit
n: Designed self-assembling icosahedral cage I32-28 dimeric subunit


分子量 (理論値)分子数
合計 (水以外)683,72040
ポリマ－683,72040
非ポリマー00
水00
1
A: Designed self-assembling icosahedral cage I32-28 trimeric subunit
B: Designed self-assembling icosahedral cage I32-28 trimeric subunit
C: Designed self-assembling icosahedral cage I32-28 trimeric subunit
D: Designed self-assembling icosahedral cage I32-28 trimeric subunit
E: Designed self-assembling icosahedral cage I32-28 trimeric subunit
F: Designed self-assembling icosahedral cage I32-28 trimeric subunit
G: Designed self-assembling icosahedral cage I32-28 trimeric subunit
H: Designed self-assembling icosahedral cage I32-28 trimeric subunit
I: Designed self-assembling icosahedral cage I32-28 trimeric subunit
J: Designed self-assembling icosahedral cage I32-28 trimeric subunit
U: Designed self-assembling icosahedral cage I32-28 dimeric subunit
V: Designed self-assembling icosahedral cage I32-28 dimeric subunit
W: Designed self-assembling icosahedral cage I32-28 dimeric subunit
X: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Y: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Z: Designed self-assembling icosahedral cage I32-28 dimeric subunit
a: Designed self-assembling icosahedral cage I32-28 dimeric subunit
b: Designed self-assembling icosahedral cage I32-28 dimeric subunit
c: Designed self-assembling icosahedral cage I32-28 dimeric subunit
d: Designed self-assembling icosahedral cage I32-28 dimeric subunit
K: Designed self-assembling icosahedral cage I32-28 trimeric subunit
L: Designed self-assembling icosahedral cage I32-28 trimeric subunit
M: Designed self-assembling icosahedral cage I32-28 trimeric subunit
N: Designed self-assembling icosahedral cage I32-28 trimeric subunit
O: Designed self-assembling icosahedral cage I32-28 trimeric subunit
P: Designed self-assembling icosahedral cage I32-28 trimeric subunit
Q: Designed self-assembling icosahedral cage I32-28 trimeric subunit
R: Designed self-assembling icosahedral cage I32-28 trimeric subunit
S: Designed self-assembling icosahedral cage I32-28 trimeric subunit
T: Designed self-assembling icosahedral cage I32-28 trimeric subunit
e: Designed self-assembling icosahedral cage I32-28 dimeric subunit
f: Designed self-assembling icosahedral cage I32-28 dimeric subunit
g: Designed self-assembling icosahedral cage I32-28 dimeric subunit
h: Designed self-assembling icosahedral cage I32-28 dimeric subunit
i: Designed self-assembling icosahedral cage I32-28 dimeric subunit
j: Designed self-assembling icosahedral cage I32-28 dimeric subunit
k: Designed self-assembling icosahedral cage I32-28 dimeric subunit
l: Designed self-assembling icosahedral cage I32-28 dimeric subunit
m: Designed self-assembling icosahedral cage I32-28 dimeric subunit
n: Designed self-assembling icosahedral cage I32-28 dimeric subunit

A: Designed self-assembling icosahedral cage I32-28 trimeric subunit
B: Designed self-assembling icosahedral cage I32-28 trimeric subunit
C: Designed self-assembling icosahedral cage I32-28 trimeric subunit
D: Designed self-assembling icosahedral cage I32-28 trimeric subunit
E: Designed self-assembling icosahedral cage I32-28 trimeric subunit
F: Designed self-assembling icosahedral cage I32-28 trimeric subunit
G: Designed self-assembling icosahedral cage I32-28 trimeric subunit
H: Designed self-assembling icosahedral cage I32-28 trimeric subunit
I: Designed self-assembling icosahedral cage I32-28 trimeric subunit
J: Designed self-assembling icosahedral cage I32-28 trimeric subunit
U: Designed self-assembling icosahedral cage I32-28 dimeric subunit
V: Designed self-assembling icosahedral cage I32-28 dimeric subunit
W: Designed self-assembling icosahedral cage I32-28 dimeric subunit
X: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Y: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Z: Designed self-assembling icosahedral cage I32-28 dimeric subunit
a: Designed self-assembling icosahedral cage I32-28 dimeric subunit
b: Designed self-assembling icosahedral cage I32-28 dimeric subunit
c: Designed self-assembling icosahedral cage I32-28 dimeric subunit
d: Designed self-assembling icosahedral cage I32-28 dimeric subunit
K: Designed self-assembling icosahedral cage I32-28 trimeric subunit
L: Designed self-assembling icosahedral cage I32-28 trimeric subunit
M: Designed self-assembling icosahedral cage I32-28 trimeric subunit
N: Designed self-assembling icosahedral cage I32-28 trimeric subunit
O: Designed self-assembling icosahedral cage I32-28 trimeric subunit
P: Designed self-assembling icosahedral cage I32-28 trimeric subunit
Q: Designed self-assembling icosahedral cage I32-28 trimeric subunit
R: Designed self-assembling icosahedral cage I32-28 trimeric subunit
S: Designed self-assembling icosahedral cage I32-28 trimeric subunit
T: Designed self-assembling icosahedral cage I32-28 trimeric subunit
e: Designed self-assembling icosahedral cage I32-28 dimeric subunit
f: Designed self-assembling icosahedral cage I32-28 dimeric subunit
g: Designed self-assembling icosahedral cage I32-28 dimeric subunit
h: Designed self-assembling icosahedral cage I32-28 dimeric subunit
i: Designed self-assembling icosahedral cage I32-28 dimeric subunit
j: Designed self-assembling icosahedral cage I32-28 dimeric subunit
k: Designed self-assembling icosahedral cage I32-28 dimeric subunit
l: Designed self-assembling icosahedral cage I32-28 dimeric subunit
m: Designed self-assembling icosahedral cage I32-28 dimeric subunit
n: Designed self-assembling icosahedral cage I32-28 dimeric subunit

A: Designed self-assembling icosahedral cage I32-28 trimeric subunit
B: Designed self-assembling icosahedral cage I32-28 trimeric subunit
C: Designed self-assembling icosahedral cage I32-28 trimeric subunit
D: Designed self-assembling icosahedral cage I32-28 trimeric subunit
E: Designed self-assembling icosahedral cage I32-28 trimeric subunit
F: Designed self-assembling icosahedral cage I32-28 trimeric subunit
G: Designed self-assembling icosahedral cage I32-28 trimeric subunit
H: Designed self-assembling icosahedral cage I32-28 trimeric subunit
I: Designed self-assembling icosahedral cage I32-28 trimeric subunit
J: Designed self-assembling icosahedral cage I32-28 trimeric subunit
U: Designed self-assembling icosahedral cage I32-28 dimeric subunit
V: Designed self-assembling icosahedral cage I32-28 dimeric subunit
W: Designed self-assembling icosahedral cage I32-28 dimeric subunit
X: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Y: Designed self-assembling icosahedral cage I32-28 dimeric subunit
Z: Designed self-assembling icosahedral cage I32-28 dimeric subunit
a: Designed self-assembling icosahedral cage I32-28 dimeric subunit
b: Designed self-assembling icosahedral cage I32-28 dimeric subunit
c: Designed self-assembling icosahedral cage I32-28 dimeric subunit
d: Designed self-assembling icosahedral cage I32-28 dimeric subunit
K: Designed self-assembling icosahedral cage I32-28 trimeric subunit
L: Designed self-assembling icosahedral cage I32-28 trimeric subunit
M: Designed self-assembling icosahedral cage I32-28 trimeric subunit
N: Designed self-assembling icosahedral cage I32-28 trimeric subunit
O: Designed self-assembling icosahedral cage I32-28 trimeric subunit
P: Designed self-assembling icosahedral cage I32-28 trimeric subunit
Q: Designed self-assembling icosahedral cage I32-28 trimeric subunit
R: Designed self-assembling icosahedral cage I32-28 trimeric subunit
S: Designed self-assembling icosahedral cage I32-28 trimeric subunit
T: Designed self-assembling icosahedral cage I32-28 trimeric subunit
e: Designed self-assembling icosahedral cage I32-28 dimeric subunit
f: Designed self-assembling icosahedral cage I32-28 dimeric subunit
g: Designed self-assembling icosahedral cage I32-28 dimeric subunit
h: Designed self-assembling icosahedral cage I32-28 dimeric subunit
i: Designed self-assembling icosahedral cage I32-28 dimeric subunit
j: Designed self-assembling icosahedral cage I32-28 dimeric subunit
k: Designed self-assembling icosahedral cage I32-28 dimeric subunit
l: Designed self-assembling icosahedral cage I32-28 dimeric subunit
m: Designed self-assembling icosahedral cage I32-28 dimeric subunit
n: Designed self-assembling icosahedral cage I32-28 dimeric subunit


分子量 (理論値)分子数
合計 (水以外)2,051,159120
ポリマ－2,051,159120
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_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
Buried area235520 Å2
ΔGint-1636 kcal/mol
Surface area725710 Å2
手法PISA
単位格子
Length a, b, c (Å)284.170, 284.170, 640.470
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))
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 self-assembling icosahedral cage I32-28 trimeric subunit / Designed ATP:cob(I)alamin adenosyltransferase


分子量: 16798.252 Da / 分子数: 20
断片: putative ATP:cob(I)alamin adenosyltransferase residues 29-183
変異: D86E, A87D, A90L, D93A, G94L, A97V, V136K, A146I, R149A, R150A, R154L
由来タイプ: 組換発現
由来: (組換発現) Burkholderia thailandensis E264 (バクテリア)
株: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / 遺伝子: BTH_I1293, DR63_1050 / 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: Q2SZ09
#2: タンパク質
Designed self-assembling icosahedral cage I32-28 dimeric subunit


分子量: 17387.738 Da / 分子数: 20 / 断片: uncharacterized protein
変異: R35Q, F36R, T54R, W122E, K129V, R137V, E140L, R141L, K144M, E148Q
由来タイプ: 組換発現
由来: (組換発現) Deinococcus radiodurans R1 (放射線耐性)
株: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
遺伝子: DR_2006 / 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: Q9RSW5

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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: 7.28 Å3/Da / 溶媒含有率: 83.1 %
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: 12.3% PEG 1500, 18% glycerol

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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: 5.58→213.2 Å / Num. obs: 59695 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / 冗長度: 5.9 % / Biso Wilson estimate: 341.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.46
反射 シェル
解像度 (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
5.58-5.730.9731.57195.2
5.73-5.880.8471.86199.2
5.88-6.050.7462.231100
6.05-6.240.5862.951100
6.24-6.440.4563.771100
6.44-6.670.3474.911100
6.67-6.920.2676.381100
6.92-7.210.189.171100
7.21-7.530.14111.351100
7.53-7.890.11713.56199.9
7.89-8.320.08917.75199.9
8.32-8.820.06920.22199.6
8.82-9.430.06324.661100
9.43-10.190.05527.311100
10.19-11.160.0530.811100
11.16-12.480.04434.051100
12.48-14.410.04233.42199.9
14.41-17.650.03735.27199.7
17.65-24.960.03539.96199.8
24.96-213.20.02844.14199.1

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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
Rotation9.8 Å97.58 Å
Translation9.8 Å97.58 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
PHASER2.5.7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 2zhz and 3nqn, but with differences

2zhz

3nqn


解像度: 5.588→213.2 Å / SU ML: 0.76 / 交差検証法: FREE R-VALUE / σ(F): 1.94 / 位相誤差: 30.32
Rfactor反射数%反射
Rfree0.2403 5387 10.01 %
Rwork0.2259 --
obs0.2274 53801 90.01 %
溶媒の処理減衰半径: 1.2 Å / VDWプローブ半径: 1.3 Å
原子変位パラメータBiso max: 501.77 Å2 / Biso mean: 317.43 Å2 / Biso min: 223.8 Å2
精密化ステップサイクル: final / 解像度: 5.588→213.2 Å
タンパク質核酸リガンド溶媒全体
原子数44240 0 0 0 44240
残基数----6000
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00945060
X-RAY DIFFRACTIONf_angle_d1.08661460
X-RAY DIFFRACTIONf_chiral_restr0.087200
X-RAY DIFFRACTIONf_plane_restr0.0088180
X-RAY DIFFRACTIONf_dihedral_angle_d12.22615980
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 (%)
5.5877-5.65120.3852150.38631261417
5.6512-5.71760.3849420.408933337519
5.7176-5.78740.3718620.373759966133
5.7874-5.86060.38551230.3383988111156
5.8606-5.93770.3811870.35531703189094
5.9377-6.01910.39331990.376317881987100
6.0191-6.10510.38591980.366917801978100
6.1051-6.19620.3661990.351817941993100
6.1962-6.2930.34252020.319418122014100
6.293-6.39620.38771960.340117671963100
6.3962-6.50640.33651990.334117951994100
6.5064-6.62480.34492030.311918262029100
6.6248-6.75220.31341990.326417881987100
6.7522-6.890.30031970.299517681965100
6.89-7.03980.30111980.271517811979100
7.0398-7.20350.29581980.250317901988100
7.2035-7.38360.25052020.221818122014100
7.3836-7.58320.26111990.229217901989100
7.5832-7.80630.21921980.221817841982100
7.8063-8.05820.26261990.222917951994100
8.0582-8.34620.22092020.206618152017100
8.3462-8.68020.1881970.171517721969100
8.6802-9.07520.19451970.175317681965100
9.0752-9.55340.17951990.171317931992100
9.5534-10.15170.20871980.18381800199899
10.1517-10.9350.18241980.18281777197599
10.935-12.03440.18651950.16951767196299
12.0344-13.77360.20351930.18061776196999
13.7736-17.34450.21940.2111754194898
17.3445-118.31010.27461990.271773197298
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)
17.66571.18825.78050.61471.09425.7483-0.42411.415-0.0273-1.25560.4074-0.31880.32030.40150.27292.54460.2642-0.01463.21890.01822.732859.6872-79.2125.9601
28.4473-3.3537-0.00758.52450.05080.62380.4807-1.1214-0.35421.3729-0.38592.00010.2749-0.60450.37022.8611-0.12220.15213.58990.19732.587852.1701-81.705949.5299
32.60470.35973.03268.5461.43727.72990.6077-0.3125-0.97330.053-0.3703-0.89050.357-0.4932-0.19052.71250.20430.03043.4507-0.13973.027272.3367-93.881541.5299
45.09910.1264.4622.73552.77745.52540.04950.7682-1.0224-0.8381-0.26630.17620.76190.06850.00383.1831-0.0007-0.26372.97620.01762.8668103.5655-156.004926.3201
59.37841.63690.81583.1204-4.54167.2374-0.1161-0.16261.5793-0.1893-0.47780.936-1.0696-0.46740.79863.15260.07350.00813.0954-0.46853.46997.2633-136.584440.6361
67.18273.6811-1.61748.15511.89397.6072-0.0119-0.3401-0.18450.42710.12951.53631.3319-0.7727-0.58142.4773-0.1651-0.05842.54680.0873.110996.8604-159.72849.9531
77.1325-4.6328-2.57499.1188-2.62289.7788-0.06720.97351.2546-1.22440.1919-0.9804-0.70780.4577-0.14342.831-0.5327-0.04852.253-0.04773.053172.9074-192.639379.1716
80.3175-0.1287-2.746410.2706-3.747310.37310.49690.2413-0.0358-0.5377-0.3012-1.57810.68541.4587-0.21842.0484-0.2395-0.11232.3622-0.09513.538912.0674-171.9355112.5207
95.1539-1.3389-2.91377.07360.29718.18250.19660.2122-1.0330.6765-0.20140.15651.5399-0.50540.01082.72690.0375-0.20962.78370.01443.145-0.1526-102.864194.0537
109.4868-1.3423-1.58077.07841.91428.31750.0510.9121-0.1801-0.13760.3681-0.9598-0.23130.5312-0.49762.1206-0.030.18952.37180.42282.054113.1206-87.246379.9424
112.43121.72463.67014.76883.57616.1398-0.1431-1.9993-0.6790.6557-0.0848-0.06160.19560.01250.03233.3375-0.1501-0.04423.05540.03753.0607-103.3627-173.3198-22.0945
127.6670.5507-1.10867.39950.4223.58630.111.04191.1804-0.3355-0.0611-0.6876-0.82410.34090.34163.113-0.29510.33793.20610.02982.8055-97.4231-168.0527-45.6402
138.9938-1.89562.93795.05053.55345.0564-0.23321.1737-1.41260.49370.5377-0.54980.4191.3853-0.73123.5068-0.2264-0.12352.61430.0482.8509-96.9645-191.6059-37.63
145.32520.02423.09676.43340.44225.15140.1209-0.1931-0.23410.0009-0.294-1.21460.15070.50690.09923.110.2097-0.05733.045-0.40022.8804-58.7867-249.6625-22.3768
155.75022.2525-4.59657.15871.16399.4661-0.36391.25361.0462-0.09570.4550.6665-1.1933-0.96730.48363.36890.1272-0.36022.85510.03523.4406-72.3463-234.515-36.7316
165.95140.7025-2.05562.6296-1.09516.52340.0384-0.25040.4638-0.49860.3477-0.70140.01611.298-0.13282.731-0.153-0.22413.14060.22693.3763-52.1386-245.756-46.0493
175.445-3.7336-2.262410.26750.19669.4046-0.1482-1.5938-0.05111.14140.02941.19690.4047-0.49730.30522.089-0.0571-0.03193.1939-0.01442.9589-11.7215-241.4984-75.2465
187.5062-7.1154-2.95295.7196-1.17998.3941-0.1328-0.2982-1.1270.50590.41031.13291.6345-0.2896-0.65882.0382-0.3616-0.15472.0525-0.05993.33810.7992-178.4288-108.5833
197.9896-4.03270.27388.6911-3.721510.0233-0.07310.5778-0.01090.2063-0.0799-1.21980.321.83410.26282.6456-0.2583-0.06412.6561-0.1732.9519-52.9186-133.3986-90.0879
207.95431.6968-0.51328.8873-0.83589.21210.6549-0.345-0.68050.6104-0.11140.42660.3817-1.0209-0.76692.3136-0.13340.35362.1941-0.00732.2719-73.0758-137.0117-75.9792
212.48853.33576.94847.87032.20728.06460.149-1.1591.12320.3555-0.4643-0.5738-0.7027-2.1760.02843.49250.51310.32283.67310.13043.749962.1305-54.250720.2492
2211.34686.8838-4.72712.1763-2.2026.75720.1595-0.5079-0.3782-0.3101-0.243-0.54160.06640.01650.24213.20310.4078-0.0063.0872-0.11692.618657.2504-68.587971.9245
236.5728-1.4944-1.97499.365-0.18523.31580.03190.33270.0960.0193-0.1386-1.2245-0.98460.9378-0.00983.01530.1472-0.19443.68960.15613.464798.5433-88.308241.7304
245.59028.67615.87578.78878.767910.436-0.0762-1.1961-0.93430.3577-0.5617-0.887-1.0411-1.16511.14473.96320.19350.21473.65690.03163.5867126.2398-151.527915.411
256.2118-5.70961.29647.11150.90221.3450.21750.17450.1413-0.98170.16430.431-0.0010.1305-0.43733.3183-0.3332-0.00722.6358-0.34083.1228111.1604-119.287255.6016
267.31764.1286-7.09545.3052-7.59028.2991-0.40470.2449-0.1227-0.58180.1083-1.36030.10251.2999-0.07953.43020.09260.03843.0645-0.173.3557114.8771-174.116863.4526
276.08374.6615-0.94918.5748-4.95148.9814-0.6382-0.3783-0.5257-0.02290.8194-0.62060.7569-0.3467-0.60152.5972-0.21880.09462.6257-0.37572.858594.7903-183.849491.8523
289.8448-4.3896-3.73083.08155.543510.86870.7695-1.2221-0.54690.73110.2485-0.29380.14220.4097-0.99672.3211-0.2221-0.33442.25060.01643.205130.3437-173.6298131.6575
291.42521.49572.662810.4136-0.28953.2793-0.1607-0.61390.7698-0.65320.0425-0.5087-1.0941-0.29050.11412.99610.09880.14323.39640.22673.36657.6404-101.8626119.4032
308.2585-0.141-5.37299.47432.18236.63450.0281-0.2929-0.67161.1305-0.59150.0865-0.8850.0023-0.01432.6643-0.1470.02492.70560.16652.853123.5526-63.010783.9373
317.3478-0.68533.50240.64132.93966.8374-0.66921.5084-1.2639-0.60460.91691.3899-1.52630.51950.06673.93590.22120.26943.1192-0.02843.1612-126.0931-162.9071-16.3084
3210.39159.0741-4.32814.94-3.62556.2743-0.8730.7684-0.6447-0.37210.66460.16510.06830.3330.27313.64140.1468-0.2063.1430.00112.8422-111.3422-165.9369-67.9647
338.5249-5.47430.228.5909-0.62081.1182-0.1333-0.1779-0.05390.20740.03830.67950.6453-1.0912-0.03653.6154-0.31980.19563.3055-0.22633.1385-114.9001-211.5351-37.8175
3410.63723.19822.32493.8759-2.45317.0918-0.35161.0259-0.45-0.4138-0.5415-0.13860.18860.49540.63573.55240.24760.16443.3650.06223.245-73.9753-267.1167-11.4505
354.3748-3.28190.62219.8782.2963.76-0.4021-0.3642-0.039-0.36540.7537-0.5975-0.0528-0.06130.11352.67790.0009-0.44623.74970.27493.1803-94.3241-237.9286-51.6889
366.99026.0169-6.79375.9540.01625.7070.1946-0.2774-0.2878-0.4324-0.27511.0410.9231-0.3079-0.09433.17010.3303-0.01413.14310.09253.239-48.6658-268.5583-59.5644
379.44783.0659-2.44335.09982.170910.75420.4847-0.523-0.874-1.0026-0.069-0.13520.54750.6306-0.12452.3695-0.0223-0.24882.70510.15292.7114-30.2312-255.9761-87.9064
381.53991.94091.486510.0974-5.02438.19210.81260.72250.0595-0.85540.48320.50351.02640.3755-1.12652.2963-0.15470.02822.4657-0.2793.5192-6.8432-195.2052-127.7629
398.8561-4.18421.82743.77820.59611.3672-0.3941-0.03050.3566-0.37710.18140.8147-0.558-0.46560.13893.1667-0.13080.25152.9264-0.07153.1953-57.6995-139.605-115.4493
407.12733.2783-3.066611.082-10.59198.82760.18541.2518-0.1299-0.26160.63840.0918-0.4238-1.2994-0.19782.61670.01030.16732.9167-0.27063.0563-99.2361-133.9333-79.9892
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA27 - 178
2X-RAY DIFFRACTION2chain BB27 - 178
3X-RAY DIFFRACTION3chain CC27 - 178
4X-RAY DIFFRACTION4chain DD27 - 178
5X-RAY DIFFRACTION5chain EE27 - 178
6X-RAY DIFFRACTION6chain FF27 - 178
7X-RAY DIFFRACTION7chain GG27 - 178
8X-RAY DIFFRACTION8chain HH27 - 178
9X-RAY DIFFRACTION9chain II27 - 178
10X-RAY DIFFRACTION10chain JJ27 - 178
11X-RAY DIFFRACTION11chain KK27 - 178
12X-RAY DIFFRACTION12chain LL27 - 178
13X-RAY DIFFRACTION13chain MM27 - 178
14X-RAY DIFFRACTION14chain NN27 - 178
15X-RAY DIFFRACTION15chain OO27 - 178
16X-RAY DIFFRACTION16chain PP27 - 178
17X-RAY DIFFRACTION17chain QQ27 - 178
18X-RAY DIFFRACTION18chain RR27 - 178
19X-RAY DIFFRACTION19chain SS27 - 178
20X-RAY DIFFRACTION20chain TT27 - 178
21X-RAY DIFFRACTION21chain UU3 - 157
22X-RAY DIFFRACTION22chain VV3 - 157
23X-RAY DIFFRACTION23chain WW3 - 157
24X-RAY DIFFRACTION24chain XX3 - 157
25X-RAY DIFFRACTION25chain YY3 - 157
26X-RAY DIFFRACTION26chain ZZ3 - 157
27X-RAY DIFFRACTION27chain aa3 - 157
28X-RAY DIFFRACTION28chain bb3 - 157
29X-RAY DIFFRACTION29chain cc3 - 157
30X-RAY DIFFRACTION30chain dd3 - 157
31X-RAY DIFFRACTION31chain ee3 - 157
32X-RAY DIFFRACTION32chain ff3 - 157
33X-RAY DIFFRACTION33chain gg3 - 157
34X-RAY DIFFRACTION34chain hh3 - 157
35X-RAY DIFFRACTION35chain ii3 - 157
36X-RAY DIFFRACTION36chain jj3 - 157
37X-RAY DIFFRACTION37chain kk3 - 157
38X-RAY DIFFRACTION38chain ll3 - 157
39X-RAY DIFFRACTION39chain mm3 - 157
40X-RAY DIFFRACTION40chain nn3 - 157

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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