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- PDB-6yf7: Virus-like particle of bacteriophage AC -

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IDまたはキーワード:

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基本情報

登録情報
データベース: PDB / ID: 6yf7
タイトルVirus-like particle of bacteriophage AC
要素Coat protein
キーワードVIRUS LIKE PARTICLE / virus / virus-like particle / structural protein
機能・相同性viral capsid / Coat protein
機能・相同性情報
生物種Marine phage AC (ファージ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.4 Å
データ登録者Rumnieks, J. / Kalnins, G. / Sisovs, M. / Lieknina, I. / Tars, K.
資金援助 Latvia, 1件
組織認可番号国
European Regional Development Fund1.1.1.1/16/A/104 Latvia
引用ジャーナル: Sci Adv / 年: 2020
タイトル: Three-dimensional structure of 22 uncultured ssRNA bacteriophages: Flexibility of the coat protein fold and variations in particle shapes.
著者: Rumnieks, J. / Lieknina, I. / Kalnins, G. / Sisovs, M. / Akopjana, I. / Bogans, J. / Tars, K.
履歴
登録2020年3月26日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年9月2日Provider: repository / タイプ: Initial release
改定 1.12020年12月16日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
改定 1.22024年1月24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
AA: Coat protein
AB: Coat protein
AC: Coat protein
AD: Coat protein
AE: Coat protein
AF: Coat protein
AG: Coat protein
AH: Coat protein
AI: Coat protein
AJ: Coat protein
AK: Coat protein
AL: Coat protein
AM: Coat protein
AN: Coat protein
AO: Coat protein
AP: Coat protein
AQ: Coat protein
AR: Coat protein
AS: Coat protein
AT: Coat protein
AU: Coat protein
AV: Coat protein
AW: Coat protein
AX: Coat protein
AY: Coat protein
AZ: Coat protein
BA: Coat protein
BB: Coat protein
BC: Coat protein
BD: Coat protein
BE: Coat protein
BF: Coat protein
BG: Coat protein
BH: Coat protein
BI: Coat protein
BJ: Coat protein
BK: Coat protein
BL: Coat protein
BM: Coat protein
BN: Coat protein
BO: Coat protein
BP: Coat protein
BQ: Coat protein
BR: Coat protein
BS: Coat protein
BT: Coat protein
BU: Coat protein
BV: Coat protein
BW: Coat protein
BX: Coat protein
BY: Coat protein
BZ: Coat protein
CA: Coat protein
CB: Coat protein
CC: Coat protein
CD: Coat protein
CE: Coat protein
CF: Coat protein
CG: Coat protein
CH: Coat protein
CI: Coat protein
CJ: Coat protein
CK: Coat protein
CL: Coat protein
CM: Coat protein
CN: Coat protein
CO: Coat protein
CP: Coat protein
CQ: Coat protein
CR: Coat protein
CS: Coat protein
CT: Coat protein
CU: Coat protein
CV: Coat protein
CW: Coat protein
CX: Coat protein
CY: Coat protein
CZ: Coat protein
DA: Coat protein
DB: Coat protein
DC: Coat protein
DD: Coat protein
DE: Coat protein
DF: Coat protein
DG: Coat protein
DH: Coat protein
DI: Coat protein
DJ: Coat protein
DK: Coat protein
DL: Coat protein
DM: Coat protein
DN: Coat protein
DO: Coat protein
DP: Coat protein
DQ: Coat protein
DR: Coat protein
DS: Coat protein
DT: Coat protein
DU: Coat protein
DV: Coat protein
DW: Coat protein
DX: Coat protein
DY: Coat protein
DZ: Coat protein
EA: Coat protein
EB: Coat protein
EC: Coat protein
ED: Coat protein
EE: Coat protein
EF: Coat protein
EG: Coat protein
EH: Coat protein
EI: Coat protein
EJ: Coat protein
EK: Coat protein
EL: Coat protein
EM: Coat protein
EN: Coat protein
EO: Coat protein
EP: Coat protein
EQ: Coat protein
ER: Coat protein
ES: Coat protein
ET: Coat protein
EU: Coat protein
EV: Coat protein
EW: Coat protein
EX: Coat protein
EY: Coat protein
EZ: Coat protein
FA: Coat protein
FB: Coat protein
FC: Coat protein
FD: Coat protein
FE: Coat protein
FF: Coat protein
FG: Coat protein
FH: Coat protein
FI: Coat protein
FJ: Coat protein
FK: Coat protein
FL: Coat protein
FM: Coat protein
FN: Coat protein
FO: Coat protein
FP: Coat protein
FQ: Coat protein
FR: Coat protein
FS: Coat protein
FT: Coat protein
FU: Coat protein
FV: Coat protein
FW: Coat protein
FX: Coat protein
FY: Coat protein
FZ: Coat protein
GA: Coat protein
GB: Coat protein
GC: Coat protein
GD: Coat protein
GE: Coat protein
GF: Coat protein
GG: Coat protein
GH: Coat protein
GI: Coat protein
GJ: Coat protein
GK: Coat protein
GL: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GP: Coat protein
GQ: Coat protein
GR: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GV: Coat protein
GW: Coat protein
GX: Coat protein
GY: Coat protein
GZ: Coat protein
HA: Coat protein
HB: Coat protein
HC: Coat protein
HD: Coat protein
HE: Coat protein
HF: Coat protein
HG: Coat protein
HH: Coat protein
HI: Coat protein
HJ: Coat protein
HK: Coat protein
HL: Coat protein
HM: Coat protein
HN: Coat protein
HO: Coat protein
HP: Coat protein
HQ: Coat protein
HR: Coat protein
HS: Coat protein
HT: Coat protein
HU: Coat protein
HV: Coat protein
HW: Coat protein
HX: Coat protein
HY: Coat protein
HZ: Coat protein
IA: Coat protein
IB: Coat protein
IC: Coat protein
ID: Coat protein
IE: Coat protein
IF: Coat protein
IG: Coat protein
IH: Coat protein
II: Coat protein
IJ: Coat protein
IK: Coat protein
IL: Coat protein
IM: Coat protein
IN: Coat protein
IO: Coat protein
IP: Coat protein
IQ: Coat protein
IR: Coat protein
IS: Coat protein
IT: Coat protein
IU: Coat protein
IV: Coat protein
IW: Coat protein
IX: Coat protein
IY: Coat protein
IZ: Coat protein
JA: Coat protein
JB: Coat protein
JC: Coat protein
JD: Coat protein
JE: Coat protein
JF: Coat protein
JG: Coat protein
JH: Coat protein
JI: Coat protein
JJ: Coat protein
JK: Coat protein
JL: Coat protein
JM: Coat protein
JN: Coat protein
JO: Coat protein
JP: Coat protein
JQ: Coat protein
JR: Coat protein
JS: Coat protein
JT: Coat protein
JU: Coat protein
JV: Coat protein
JW: Coat protein
JX: Coat protein
JY: Coat protein
JZ: Coat protein
KA: Coat protein
KB: Coat protein
KC: Coat protein
KD: Coat protein
KE: Coat protein
KF: Coat protein
KG: Coat protein
KH: Coat protein
KI: Coat protein
KJ: Coat protein


分子量 (理論値)分子数
合計 (水以外)3,317,206270
ポリマ－3,317,206270
非ポリマー00
水00
1
AA: Coat protein
AB: Coat protein
AC: Coat protein
AD: Coat protein
AE: Coat protein
AF: Coat protein
AG: Coat protein
AH: Coat protein
AI: Coat protein
AJ: Coat protein
AK: Coat protein
AL: Coat protein
AM: Coat protein
AN: Coat protein
AO: Coat protein
AP: Coat protein
AQ: Coat protein
AR: Coat protein
AS: Coat protein
AT: Coat protein
AU: Coat protein
AV: Coat protein
AW: Coat protein
AX: Coat protein
AY: Coat protein
AZ: Coat protein
BA: Coat protein
BB: Coat protein
BC: Coat protein
BD: Coat protein
BE: Coat protein
BF: Coat protein
BG: Coat protein
BH: Coat protein
BI: Coat protein
BJ: Coat protein
BK: Coat protein
BL: Coat protein
BM: Coat protein
BN: Coat protein
BO: Coat protein
BP: Coat protein
BQ: Coat protein
BR: Coat protein
BS: Coat protein
BT: Coat protein
BU: Coat protein
BV: Coat protein
BW: Coat protein
BX: Coat protein
BY: Coat protein
BZ: Coat protein
CA: Coat protein
CB: Coat protein
CC: Coat protein
CD: Coat protein
CE: Coat protein
CF: Coat protein
CG: Coat protein
CH: Coat protein
CI: Coat protein
CJ: Coat protein
CK: Coat protein
CL: Coat protein
CM: Coat protein
CN: Coat protein
CO: Coat protein
CP: Coat protein
CQ: Coat protein
CR: Coat protein
CS: Coat protein
CT: Coat protein
CU: Coat protein
CV: Coat protein
CW: Coat protein
CX: Coat protein
CY: Coat protein
CZ: Coat protein
DA: Coat protein
DB: Coat protein
DC: Coat protein
DD: Coat protein
DE: Coat protein
DF: Coat protein
DG: Coat protein
DH: Coat protein
DI: Coat protein
DJ: Coat protein
DK: Coat protein
DL: Coat protein
DM: Coat protein
DN: Coat protein
DO: Coat protein
DP: Coat protein
DQ: Coat protein
DR: Coat protein
DS: Coat protein
DT: Coat protein
DU: Coat protein
DV: Coat protein
DW: Coat protein
DX: Coat protein
DY: Coat protein
DZ: Coat protein
EA: Coat protein
EB: Coat protein
EC: Coat protein
ED: Coat protein
EE: Coat protein
EF: Coat protein
EG: Coat protein
EH: Coat protein
EI: Coat protein
EJ: Coat protein
EK: Coat protein
EL: Coat protein
EM: Coat protein
EN: Coat protein
EO: Coat protein
EP: Coat protein
EQ: Coat protein
ER: Coat protein
ES: Coat protein
ET: Coat protein
EU: Coat protein
EV: Coat protein
EW: Coat protein
EX: Coat protein
EY: Coat protein
EZ: Coat protein
FA: Coat protein
FB: Coat protein
FC: Coat protein
FD: Coat protein
FE: Coat protein
FF: Coat protein
FG: Coat protein
FH: Coat protein
FI: Coat protein
FJ: Coat protein
FK: Coat protein
FL: Coat protein
FM: Coat protein
FN: Coat protein
FO: Coat protein
FP: Coat protein
FQ: Coat protein
FR: Coat protein
FS: Coat protein
FT: Coat protein
FU: Coat protein
FV: Coat protein
FW: Coat protein
FX: Coat protein
FY: Coat protein
FZ: Coat protein
GA: Coat protein
GB: Coat protein
GC: Coat protein
GD: Coat protein
GE: Coat protein
GF: Coat protein
GG: Coat protein
GH: Coat protein
GI: Coat protein
GJ: Coat protein
GK: Coat protein
GL: Coat protein
GM: Coat protein
GN: Coat protein
GO: Coat protein
GP: Coat protein
GQ: Coat protein
GR: Coat protein
GS: Coat protein
GT: Coat protein
GU: Coat protein
GV: Coat protein
GW: Coat protein
GX: Coat protein


分子量 (理論値)分子数
合計 (水以外)2,211,470180
ポリマ－2,211,470180
非ポリマー00
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area691310 Å2
ΔGint-5159 kcal/mol
Surface area837130 Å2
手法PISA
2
GY: Coat protein
GZ: Coat protein
HA: Coat protein
HB: Coat protein
HC: Coat protein
HD: Coat protein
HE: Coat protein
HF: Coat protein
HG: Coat protein
HH: Coat protein
HI: Coat protein
HJ: Coat protein
HK: Coat protein
HL: Coat protein
HM: Coat protein
HN: Coat protein
HO: Coat protein
HP: Coat protein
HQ: Coat protein
HR: Coat protein
HS: Coat protein
HT: Coat protein
HU: Coat protein
HV: Coat protein
HW: Coat protein
HX: Coat protein
HY: Coat protein
HZ: Coat protein
IA: Coat protein
IB: Coat protein
IC: Coat protein
ID: Coat protein
IE: Coat protein
IF: Coat protein
IG: Coat protein
IH: Coat protein
II: Coat protein
IJ: Coat protein
IK: Coat protein
IL: Coat protein
IM: Coat protein
IN: Coat protein
IO: Coat protein
IP: Coat protein
IQ: Coat protein
IR: Coat protein
IS: Coat protein
IT: Coat protein
IU: Coat protein
IV: Coat protein
IW: Coat protein
IX: Coat protein
IY: Coat protein
IZ: Coat protein
JA: Coat protein
JB: Coat protein
JC: Coat protein
JD: Coat protein
JE: Coat protein
JF: Coat protein
JG: Coat protein
JH: Coat protein
JI: Coat protein
JJ: Coat protein
JK: Coat protein
JL: Coat protein
JM: Coat protein
JN: Coat protein
JO: Coat protein
JP: Coat protein
JQ: Coat protein
JR: Coat protein
JS: Coat protein
JT: Coat protein
JU: Coat protein
JV: Coat protein
JW: Coat protein
JX: Coat protein
JY: Coat protein
JZ: Coat protein
KA: Coat protein
KB: Coat protein
KC: Coat protein
KD: Coat protein
KE: Coat protein
KF: Coat protein
KG: Coat protein
KH: Coat protein
KI: Coat protein
KJ: Coat protein

GY: Coat protein
GZ: Coat protein
HA: Coat protein
HB: Coat protein
HC: Coat protein
HD: Coat protein
HE: Coat protein
HF: Coat protein
HG: Coat protein
HH: Coat protein
HI: Coat protein
HJ: Coat protein
HK: Coat protein
HL: Coat protein
HM: Coat protein
HN: Coat protein
HO: Coat protein
HP: Coat protein
HQ: Coat protein
HR: Coat protein
HS: Coat protein
HT: Coat protein
HU: Coat protein
HV: Coat protein
HW: Coat protein
HX: Coat protein
HY: Coat protein
HZ: Coat protein
IA: Coat protein
IB: Coat protein
IC: Coat protein
ID: Coat protein
IE: Coat protein
IF: Coat protein
IG: Coat protein
IH: Coat protein
II: Coat protein
IJ: Coat protein
IK: Coat protein
IL: Coat protein
IM: Coat protein
IN: Coat protein
IO: Coat protein
IP: Coat protein
IQ: Coat protein
IR: Coat protein
IS: Coat protein
IT: Coat protein
IU: Coat protein
IV: Coat protein
IW: Coat protein
IX: Coat protein
IY: Coat protein
IZ: Coat protein
JA: Coat protein
JB: Coat protein
JC: Coat protein
JD: Coat protein
JE: Coat protein
JF: Coat protein
JG: Coat protein
JH: Coat protein
JI: Coat protein
JJ: Coat protein
JK: Coat protein
JL: Coat protein
JM: Coat protein
JN: Coat protein
JO: Coat protein
JP: Coat protein
JQ: Coat protein
JR: Coat protein
JS: Coat protein
JT: Coat protein
JU: Coat protein
JV: Coat protein
JW: Coat protein
JX: Coat protein
JY: Coat protein
JZ: Coat protein
KA: Coat protein
KB: Coat protein
KC: Coat protein
KD: Coat protein
KE: Coat protein
KF: Coat protein
KG: Coat protein
KH: Coat protein
KI: Coat protein
KJ: Coat protein


分子量 (理論値)分子数
合計 (水以外)2,211,470180
ポリマ－2,211,470180
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_555-x,y,-z1
Buried area691340 Å2
ΔGint-5159 kcal/mol
Surface area837090 Å2
手法PISA
単位格子
Length a, b, c (Å)432.290, 307.870, 679.449
Angle α, β, γ (deg.)90.000, 107.150, 90.000
Int Tables number5
Space group name H-MC121

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要素

#1: タンパク質 ...
Coat protein


分子量: 12285.947 Da / 分子数: 270 / 由来タイプ: 組換発現 / 由来: (組換発現) Marine phage AC (ファージ) / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A068EP60

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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: 6.51 Å3/Da / 溶媒含有率: 81.11 %
結晶化温度: 293 K / 手法: 蒸気拡散法, シッティングドロップ法 / 詳細: 0.85 M ammonium sulfate

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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: MAX II / ビームライン: I911-3 / 波長: 0.97934 Å
検出器タイプ: MARMOSAIC 225 mm CCD / 検出器: CCD / 日付: 2015年11月5日
放射モノクロメーター: Double crystal monochromator, Si(111)
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: 0.97934 Å / 相対比: 1
反射解像度: 3.4→44.262 Å / Num. obs: 591127 / % possible obs: 51.1 % / 冗長度: 1.8 % / CC1/2: 0.965 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.168 / Rrim(I) all: 0.261 / Net I/av σ(I): 3.4 / Net I/σ(I): 3.3
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
3.4-3.581.70.7491133407797750.630.9840.749147.3
3.58-3.81.70.5531.3132715763040.4790.7350.5531.547.8
3.8-4.061.70.3951.8124305719220.3430.5260.3951.948
4.06-4.391.70.272.8117223682980.2340.3590.272.748.9
4.39-4.811.70.1843.9111149651370.1590.2440.1843.750.6
4.81-5.381.70.1724.1107814622920.1490.2290.1723.853.6
5.38-6.211.80.174.2106944583200.1460.2250.173.956.9
6.21-7.620.1414.9103431505140.1160.1840.1414.858.2
7.6-10.752.20.0797.688277392940.0610.10.079858.6
10.75-44.2622.30.0411244156192710.0310.0520.0419.752.3

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解析

ソフトウェア
名称バージョン分類
MOSFLMデータ削減
SCALA3.3.22データスケーリング
FFT位相決定
PHENIX1.14_3260精密化
PDB_EXTRACT3.25データ抽出
精密化構造決定の手法: 分子置換
開始モデル: 2ms2

2ms2


解像度: 3.4→44.262 Å / SU ML: 0.59 / 交差検証法: THROUGHOUT / σ(F): 1.34 / 位相誤差: 29.58
Rfactor反射数%反射
Rfree0.27 29845 5.05 %
Rwork0.2681 --
obs0.2682 590873 50.94 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
原子変位パラメータBiso max: 240.43 Å2 / Biso mean: 69.7779 Å2 / Biso min: 5.82 Å2
精密化ステップサイクル: final / 解像度: 3.4→44.262 Å
タンパク質核酸リガンド溶媒全体
原子数231390 0 0 0 231390
残基数----30780
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.4-3.43860.40638890.40991689946
3.4386-3.47910.42218110.40511725747
3.4791-3.52150.4029290.39941736147
3.5215-3.5660.38629780.38741745448
3.566-3.61290.38719380.38851743048
3.6129-3.66240.38488910.38521736647
3.6624-3.71470.37238810.3811764248
3.7147-3.77010.37899280.36631749148
3.7701-3.8290.35288850.35421748548
3.829-3.89170.36078990.35181747548
3.8917-3.95880.34169040.34411752248
3.9588-4.03070.32129830.32551748448
4.0307-4.10820.3179520.31711766748
4.1082-4.1920.29439280.30191777948
4.192-4.28310.28559710.2961788249
4.2831-4.38260.27689150.2811800049
4.3826-4.49210.263710650.26561812750
4.4921-4.61350.275110510.26171835450
4.6135-4.74910.255810570.25321866851
4.7491-4.90220.249710470.24941905752
4.9022-5.07710.23529890.24011945053
5.0771-5.28010.256810830.2371978354
5.2801-5.520.24110490.23582040455
5.52-5.81040.23711010.23082066556
5.8104-6.17360.227111350.21952110757
6.1736-6.64880.220511180.21362131658
6.6488-7.31520.196411540.19692134158
7.3152-8.36750.16411240.16062145858
8.3675-10.51870.13211550.13962149058
10.5187-44.2620.225310350.20631961453

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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

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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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