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- PDB-9prr: X-ray crystal structure of Streptomyces cacaoi PolF in complex wi... -

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基本情報

登録情報
データベース: PDB / ID: 9prr
タイトルX-ray crystal structure of Streptomyces cacaoi PolF in complex with iron and L-isoleucine
要素PolF
キーワードOXIDOREDUCTASE / polyoximic acid / diiron cofactor / biosynthesis / cyclization / heme-oxygenase-like diiron enzyme / BIOSYNTHETIC PROTEIN
機能・相同性: / ISOLEUCINE
機能・相同性情報
生物種Streptomyces cacaoi (バクテリア)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.06 Å
データ登録者Blancas Cortez, J.J. / Boal, A.K.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R35GM119707 米国
引用ジャーナル: To Be Published
タイトル: Azetidine amino acid biosynthesis by non-heme iron-dependent enzymes
著者: Du, Y. / Thanapipatsiri, A. / Salas Sola, X.E. / Blancas Cortez, J.J. / Lin, C.Y. / Boal, A.K. / Krebs, C. / Bollinger, J.M. / Yokoyama, K.
履歴
登録2025年7月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02025年10月15日Provider: repository / タイプ: Initial release

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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: PolF
B: PolF
C: PolF
D: PolF
E: PolF
F: PolF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)183,10635
ポリマ－181,0086
非ポリマー2,09929
水2,522140
1
A: PolF
F: PolF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,04412
ポリマ－60,3362
非ポリマー70810
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4220 Å2
ΔGint-164 kcal/mol
Surface area22120 Å2
手法PISA
2
B: PolF
C: PolF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,04412
ポリマ－60,3362
非ポリマー70810
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-142 kcal/mol
Surface area22030 Å2
手法PISA
3
D: PolF
E: PolF
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)61,01811
ポリマ－60,3362
非ポリマー6829
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-139 kcal/mol
Surface area22290 Å2
手法PISA
単位格子
Length a, b, c (Å)78.586, 143.628, 81.447
Angle α, β, γ (deg.)90.000, 109.777, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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要素

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タンパク質 , 1種, 6分子 ABCDEF

#1: タンパク質
PolF


分子量: 30167.922 Da / 分子数: 6 / 由来タイプ: 組換発現
詳細: The originally expressed polypeptide construct possessed the extra sequence MGSSHHHHHHSSGLVPRGSHGENLYFQ at the N-terminus. This sequence included a His6, thrombin recognition, TEV-recognition ...詳細: The originally expressed polypeptide construct possessed the extra sequence MGSSHHHHHHSSGLVPRGSHGENLYFQ at the N-terminus. This sequence included a His6, thrombin recognition, TEV-recognition sequence, and linkers between them. This extra sequence was cleaved off the construct through TEV incubation and removed from protein solution through Ni-NTA and S200 purification.
由来: (組換発現) Streptomyces cacaoi (バクテリア)
発現宿主: Escherichia coli BL21(DE3) (大腸菌)

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非ポリマー , 5種, 169分子

#2: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C3H8O3
#3: 化合物
ChemComp-FE2 / FE (II) ION


分子量: 55.845 Da / 分子数: 12 / 由来タイプ: 合成 / 式: Fe / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 11 / 由来タイプ: 合成 / 式: Zn
#5: 化合物
ChemComp-ILE / ISOLEUCINE


タイプ: L-peptide linking / 分子量: 131.173 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C6H13NO2 / タイプ: SUBJECT OF INVESTIGATION
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 140 / 由来タイプ: 天然 / 式: H2O

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詳細

研究の焦点であるリガンドがあるかY
Has protein modificationN

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶マシュー密度: 2.39 Å3/Da / 溶媒含有率: 48.53 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.5 M Lithium Chloride, 0.1 M Tris PH 7.6, 15% (w/v) PEG 6000

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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: NSLS-II / ビームライン: 17-ID-1 / 波長: 0.919689 Å
検出器タイプ: DECTRIS EIGER X 9M / 検出器: PIXEL / 日付: 2025年6月13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: 0.919689 Å / 相対比: 1
反射解像度: 2.06→34.16 Å / Num. obs: 51376 / % possible obs: 91.69 % / 冗長度: 6.81 % / Biso Wilson estimate: 27.27 Å2 / CC1/2: 0.973 / Net I/σ(I): 7.6
反射 シェル解像度: 2.06→2.7 Å / Num. unique obs: 5703 / CC1/2: 0.67

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解析

ソフトウェア
名称バージョン分類
PHENIX1.21.1.5286精密化
XDSデータ削減
Aimlessデータスケーリング
PHENIX位相決定
精密化構造決定の手法: 分子置換 / 解像度: 2.06→34.16 Å / SU ML: 0.1964 / 交差検証法: FREE R-VALUE / σ(F): 1.34 / 位相誤差: 27.8316
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2346 1993 3.89 %
Rwork0.1959 49283 -
obs0.1974 51276 49.1 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.1 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 30.41 Å2
精密化ステップサイクル: LAST / 解像度: 2.06→34.16 Å
タンパク質核酸リガンド溶媒全体
原子数12380 0 71 140 12591
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002912671
X-RAY DIFFRACTIONf_angle_d0.555917214
X-RAY DIFFRACTIONf_chiral_restr0.03871926
X-RAY DIFFRACTIONf_plane_restr0.00492282
X-RAY DIFFRACTIONf_dihedral_angle_d14.5144430
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.1100.54889X-RAY DIFFRACTION0.12
2.11-2.170.582720.487751X-RAY DIFFRACTION0.73
2.17-2.230.535130.455770X-RAY DIFFRACTION0.99
2.23-2.310.332420.402956X-RAY DIFFRACTION0.78
2.31-2.380.117920.321765X-RAY DIFFRACTION0.99
2.4-2.480.241570.2705128X-RAY DIFFRACTION2.2
2.49-2.60.3225650.25861653X-RAY DIFFRACTION23.19
2.6-2.730.27971880.26044637X-RAY DIFFRACTION64.68
2.73-2.910.26672750.24256852X-RAY DIFFRACTION95.41
2.91-3.130.28552900.22617156X-RAY DIFFRACTION100
3.13-3.440.2422880.217109X-RAY DIFFRACTION99.21
3.44-3.940.23792900.18837042X-RAY DIFFRACTION97.98
3.94-4.960.2062860.15727187X-RAY DIFFRACTION99.83
4.96-34.160.19612950.17187268X-RAY DIFFRACTION99.85
精密化 TLS手法: refined / Origin x: 37.905 Å / Origin y: 17.042 Å / Origin z: -23.093 Å
111213212223313233
T0.084100489560786 Å2-0.012597434096985 Å20.02882471188469 Å2-0.13355548033253 Å2-0.0046730667173839 Å2--0.13651061589341 Å2
L0.30828802645721 °20.0060026409432283 °20.21298421152054 °2-0.35744238701922 °2-0.024093875274745 °2--0.70543045232371 °2
S0.0027781494545141 Å °-0.055612011637048 Å °0.0547 Å °0.0068844926665461 Å °-0.0049136900457832 Å °0.004 Å °-0.01167063834319 Å °0.02126027812126 Å °0.00532 Å °
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )A7 - 275
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )A301
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )A302 - 303
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )A401 - 427
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )A304 - 305
6X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )B7 - 275
7X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )B301
8X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )B302 - 303
9X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )B401 - 423
10X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )B304 - 305
11X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )C7 - 275
12X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )C301
13X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )C302 - 303
14X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )C401 - 424
15X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )C304 - 305
16X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )D7 - 275
17X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )D301
18X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )D302 - 303
19X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )D401 - 417
20X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )D304
21X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )E6 - 275
22X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )E301
23X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )E302 - 303
24X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )E401 - 430
25X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )E304 - 305
26X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )F12 - 275
27X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )F301
28X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )F302 - 303
29X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )F401 - 419
30X-RAY DIFFRACTION1( CHAIN A AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:427 OR RESID 304:305 ) ) OR ( CHAIN B AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:423 OR RESID 304:305 ) ) OR ( CHAIN C AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:424 OR RESID 304:305 ) ) OR ( CHAIN D AND ( RESID 7:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:417 OR RESID 304:304 ) ) OR ( CHAIN E AND ( RESID 6:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:430 OR RESID 304:305 ) ) OR ( CHAIN F AND ( RESID 12:275 OR RESID 301:301 OR RESID 302:303 OR RESID 401:419 OR RESID 304:305 ) )F304 - 305

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

他の情報も見る