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- PDB-6nhg: Rhodobacter sphaeroides Mitochondrial respiratory chain complex -

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基本情報

登録情報
データベース: PDB / ID: 6nhg
タイトルRhodobacter sphaeroides Mitochondrial respiratory chain complex
要素
  • (Cytochrome b-c1 complex subunit ...) x 9
  • Cytochrome b
  • Cytochrome c1, heme protein, mitochondrial
キーワードOXIDOREDUCTASE / Mitochondrial respiratory chain complex / cytochrome bc1 / inhibitors / electron transfer
機能・相同性
機能・相同性情報


Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane ...Complex III assembly / Respiratory electron transport / respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / mitochondrial electron transport, ubiquinol to cytochrome c / Mitochondrial protein degradation / ubiquinone binding / respiratory electron transport chain / mitochondrial membrane / metalloendopeptidase activity / 2 iron, 2 sulfur cluster binding / mitochondrial inner membrane / oxidoreductase activity / heme binding / mitochondrion / proteolysis / metal ion binding / membrane
類似検索 - 分子機能
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #220 / Cytochrome Bc1 Complex; Chain F / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit 9 / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol cytochrome reductase, transmembrane domain / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Cytochrome b-c1 complex subunit 10 / Single alpha-helix domain superfamily / Ubiquinol-cytochrome C reductase complex, 6.4kD protein / Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Ubiquinol-cytochrome c reductase 8kDa, N-terminal / Ubiquinol-cytochrome c reductase 8 kDa, N-terminal / Globular protein, non-globular alpha/beta subunit / Cytochrome b-c1 complex, subunit 6 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / Cytochrome b-c1 complex subunit 8 / UcrQ family / Cytochrome bc1 complex subunit Rieske, transmembrane domain superfamily / 3-layer Sandwich / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 7 superfamily / Ubiquinol-cytochrome C reductase complex 14kD subunit / Cytochrome b-c1 complex subunit 8 superfamily / Cytochrome b-c1 complex subunit Rieske, transmembrane domain / Ubiquinol cytochrome reductase transmembrane region / Ubiquinol-cytochrome C reductase hinge domain / Ubiquinol-cytochrome C reductase hinge domain superfamily / Ubiquinol-cytochrome C reductase hinge protein / Cytochrome b-c1 complex subunit 9 / Cytochrome b-c1 complex subunit 9 superfamily / Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like / Cytochrome c1, transmembrane anchor, C-terminal / : / Cytochrome b / Ubiquinol-cytochrome c reductase, iron-sulphur subunit / : / Cytochrome c1 / Cytochrome C1 family / : / Cytochrome b/b6, C-terminal / Cytochrome b(C-terminal)/b6/petD / Cytochrome b/b6 C-terminal region profile. / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Cytochrome b/b6, C-terminal domain superfamily / Cytochrome b/b6/petB / Rieske iron-sulphur protein, C-terminal / Cytochrome b/b6, N-terminal / Cytochrome b/b6-like domain superfamily / Cytochrome b/b6 N-terminal region profile. / Di-haem cytochrome, transmembrane / Rieske iron-sulphur protein / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix Hairpins / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8PE / Chem-AZO / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial ...1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / Chem-8PE / Chem-AZO / CARDIOLIPIN / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Cytochrome c1, heme protein, mitochondrial / Cytochrome b-c1 complex subunit 6, mitochondrial / Cytochrome b-c1 complex subunit 7 / Cytochrome b-c1 complex subunit 9 / Cytochrome b / Cytochrome b-c1 complex subunit 10 / Cytochrome b-c1 complex subunit 8 / Cytochrome b-c1 complex subunit Rieske, mitochondrial / Cytochrome b-c1 complex subunit 2, mitochondrial / Cytochrome b-c1 complex subunit 1, mitochondrial
類似検索 - 構成要素
生物種Bos taurus (ウシ)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.8 Å
データ登録者Xia, D. / Zhou, F. / Esser, L.
引用ジャーナル: J.Biol.Chem. / 年: 2019
タイトル: Crystal structure of bacterial cytochromebc1in complex with azoxystrobin reveals a conformational switch of the Rieske iron-sulfur protein subunit.
著者: Esser, L. / Zhou, F. / Yu, C.A. / Xia, D.
履歴
登録2018年12月21日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02019年6月19日Provider: repository / タイプ: Initial release
改定 1.12019年6月26日Group: Data collection / Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
改定 1.22019年8月21日Group: Data collection / Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
改定 1.32023年10月11日Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
改定 1.42024年11月13日Group: Structure summary
カテゴリ: pdbx_entry_details / pdbx_modification_feature

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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: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)250,14723
ポリマ－241,13311
非ポリマー9,01412
水61334
1
A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
ヘテロ分子

A: Cytochrome b-c1 complex subunit 1, mitochondrial
B: Cytochrome b-c1 complex subunit 2, mitochondrial
C: Cytochrome b
D: Cytochrome c1, heme protein, mitochondrial
E: Cytochrome b-c1 complex subunit Rieske, mitochondrial
F: Cytochrome b-c1 complex subunit 7
G: Cytochrome b-c1 complex subunit 8
H: Cytochrome b-c1 complex subunit 6, mitochondrial
I: Cytochrome b-c1 complex subunit Rieske, mitochondrial
J: Cytochrome b-c1 complex subunit 9
K: Cytochrome b-c1 complex subunit 10
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)500,29346
ポリマ－482,26622
非ポリマー18,02724
水21612
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation10_665-x+1,-y+1,z1
Buried area110240 Å2
ΔGint-719 kcal/mol
Surface area161620 Å2
手法PISA
単位格子
Length a, b, c (Å)154.181, 154.181, 598.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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要素

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Cytochrome b-c1 complex subunit ... , 9種, 9分子 ABEFGHIJK

#1: タンパク質 Cytochrome b-c1 complex subunit 1, mitochondrial / Complex III subunit 1 / Core protein I / Ubiquinol-cytochrome-c reductase complex core protein 1


分子量: 49266.254 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P31800
#2: タンパク質 Cytochrome b-c1 complex subunit 2, mitochondrial / Complex III subunit 2 / Core protein II / Ubiquinol-cytochrome-c reductase complex core protein 2


分子量: 46575.469 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P23004
#5: タンパク質 Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Ubiquinol-cytochrome c reductase iron-sulfur subunit


分子量: 21640.580 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P13272, quinol-cytochrome-c reductase
#6: タンパク質 Cytochrome b-c1 complex subunit 7 / Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex ...Complex III subunit 7 / Complex III subunit VII / QP-C / Ubiquinol-cytochrome c reductase complex 14 kDa protein


分子量: 13370.206 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00129
#7: タンパク質 Cytochrome b-c1 complex subunit 8 / Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa ...Complex III subunit 8 / Complex III subunit VIII / Ubiquinol-cytochrome c reductase complex 9.5 kDa protein / Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C


分子量: 9448.833 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P13271
#8: タンパク質 Cytochrome b-c1 complex subunit 6, mitochondrial / Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / ...Complex III subunit 6 / Complex III subunit VIII / Cytochrome c1 non-heme 11 kDa protein / Mitochondrial hinge protein / Ubiquinol-cytochrome c reductase complex 11 kDa protein


分子量: 9189.116 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00126
#9: タンパク質 Cytochrome b-c1 complex subunit Rieske, mitochondrial / Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / ...Complex III subunit 5 / Cytochrome b-c1 complex subunit 5 / Rieske iron-sulfur protein / RISP / Rieske protein UQCRFS1 / Ubiquinol-cytochrome c reductase iron-sulfur subunit


分子量: 7964.259 Da / 分子数: 1 / 由来タイプ: 組換発現
詳細: Amino terminal signal peptide of mitiochondrial bc1 Rieske protein
由来: (組換発現) Bos taurus (ウシ) / 遺伝子: UQCRFS1 / 発現宿主: Bos taurus (ウシ) / 参照: UniProt: P13272, quinol-cytochrome-c reductase
#10: タンパク質 Cytochrome b-c1 complex subunit 9 / Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol- ...Complex III subunit 9 / Complex III subunit X / Cytochrome c1 non-heme 7 kDa protein / Ubiquinol-cytochrome c reductase complex 7.2 kDa protein


分子量: 7338.425 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00130
#11: タンパク質 Cytochrome b-c1 complex subunit 10 / Complex III subunit 10 / Complex III subunit XI / Ubiquinol-cytochrome c reductase complex 6.4 kDa protein


分子量: 6396.408 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P07552

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タンパク質 , 2種, 2分子 CD

#3: タンパク質 Cytochrome b / Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol- ...Complex III subunit 3 / Complex III subunit III / Cytochrome b-c1 complex subunit 3 / Ubiquinol-cytochrome-c reductase complex cytochrome b subunit


分子量: 42620.340 Da / 分子数: 1 / 由来タイプ: 天然 / 由来: (天然) Bos taurus (ウシ) / 参照: UniProt: P00157
#4: タンパク質 Cytochrome c1, heme protein, mitochondrial / Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol- ...Complex III subunit 4 / Complex III subunit IV / Cytochrome b-c1 complex subunit 4 / Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit / Cytochrome c-1


分子量: 27323.277 Da / 分子数: 1 / 由来タイプ: 組換発現 / 由来: (組換発現) Bos taurus (ウシ) / 遺伝子: CYC1 / 発現宿主: Bos taurus (ウシ) / 参照: UniProt: P00125

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非ポリマー , 9種, 46分子

#12: 化合物 ChemComp-6PE / 1,2-DIHEXANOYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE / [O-(1-O,2-O-ジヘキサノイル-L-グリセロ-3-ホスホ)-2-アミノエタノ-ル]アニオン


分子量: 410.420 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C17H33NO8P
#13: 化合物 ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL


分子量: 1464.043 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C81H156O17P2 / コメント: リン脂質*YM
#14: 化合物 ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#15: 化合物 ChemComp-AZO / METHYL (2Z)-2-(2-{[6-(2-CYANOPHENOXY)PYRIMIDIN-4-YL]OXY}PHENYL)-3-METHOXYACRYLATE / AZOXYSTROBIN / アゾキシストロビン


分子量: 403.387 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C22H17N3O5
#16: 化合物 ChemComp-8PE / (2R)-3-{[(S)-(2-aminoethoxy)(hydroxy)phosphoryl]oxy}-2-(tetradecanoyloxy)propyl octadecanoate / 3-SN-PHOSPHATIDYLETHANOLAMINE


分子量: 691.959 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C37H74NO8P / コメント: リン脂質*YM
#17: 化合物 ChemComp-HEC / HEME C


分子量: 618.503 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C34H34FeN4O4
#18: 化合物 ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 1 / 由来タイプ: 合成 / 式: Fe2S2
#19: 化合物 ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


分子量: 677.933 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C36H72NO8P / コメント: リン脂質*YM
#20: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 34 / 由来タイプ: 天然 / 式: H2O

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詳細

Has protein modificationY

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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: 3.69 Å3/Da / 溶媒含有率: 66.63 %
結晶化温度: 277 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 7.2
詳細: 50 mM MOPS 7.2 pH, 20 mM Ammonium acetate, 20% glycerol. Incubation with 2-5 mol excess of Azoxystrobin. Precipitant 12% PEG4000, 0.5 M KCl, 0.1% DHPC; Protein:PPT ratio 1:0.57
Temp details: constant

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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: APS / ビームライン: 5ID-B / 波長: 1.739 Å
検出器タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2001年2月3日
放射モノクロメーター: 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: 1.739 Å / 相対比: 1
反射解像度: 2.8→30 Å / Num. obs: 167324 / % possible obs: 99.8 % / 冗長度: 23.2 % / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.022 / Rrim(I) all: 0.107 / Χ2: 1.009 / Net I/σ(I): 10
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.8515.21.18943920.8890.311.230.824100
2.85-2.924.81.40943990.9440.2871.4390.846100
2.9-2.9625.61.07344030.9650.2151.0950.757100
2.96-3.0225.60.90244090.9770.1810.920.702100
3.02-3.0825.50.83144180.9790.1670.8480.75100
3.08-3.1525.50.52844300.9850.1060.5390.786100
3.15-3.2325.30.4444110.9890.0890.4490.847100
3.23-3.3225.10.31144210.9940.0630.3170.92100
3.32-3.4224.90.2644470.9950.0530.2650.975100
3.42-3.5324.80.20244270.9960.0410.2071.055100
3.53-3.6523.70.16844220.9970.0350.1721.192100
3.65-3.823.40.16444580.9960.0340.1681.48399.9
3.8-3.9722.90.11844580.9980.0250.121.25699.8
3.97-4.1822.30.09844440.9980.0210.11.21199.8
4.18-4.4421.70.08144600.9990.0170.0831.2399.5
4.44-4.7821.30.07344540.9990.0160.0741.16799.2
4.78-5.2621.30.06544850.9990.0140.0671.17799.5
5.26-6.0221.80.06745500.9990.0140.0681.09299.9
6.02-7.5621.80.05745860.9990.0120.0591.02699.9
7.56-3021.80.04447400.9990.0090.0450.98898.1

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解析

ソフトウェア
名称バージョン分類
DENZOデータ削減
SCALEPACKデータスケーリング
PHENIX精密化
PDB_EXTRACT3.24データ抽出
PHENIX位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1SQX

1sqx


解像度: 2.8→29.87 Å / SU ML: 0.41 / 交差検証法: THROUGHOUT / σ(F): 1.33 / 位相誤差: 32.44
Rfactor反射数%反射
Rfree0.289 3731 2.23 %
Rwork0.251 --
obs0.2518 167324 98.72 %
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: 270.33 Å2 / Biso mean: 108.8564 Å2 / Biso min: 37.99 Å2
精密化ステップサイクル: final / 解像度: 2.8→29.87 Å
タンパク質核酸リガンド溶媒全体
原子数16342 0 1002 34 17378
Biso mean--120.53 57.78 -
残基数----2080
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.83540.31591400.322961146254100
2.8354-2.87270.34211360.328761346270100
2.8727-2.9120.44571410.34156063620499
2.912-2.95360.42131370.35546058619599
2.9536-2.99760.48091400.36746030617099
2.9976-3.04440.42761340.36246030616498
3.0444-3.09430.40021440.35286045618998
3.0943-3.14760.35431360.33526094623099
3.1476-3.20480.34361360.32815983611998
3.2048-3.26630.44051330.33475959609297
3.2663-3.33290.42911360.29746051618798
3.3329-3.40530.37991320.31246018615098
3.4053-3.48440.28921360.28986051618799
3.4844-3.57140.3261400.27116082622299
3.5714-3.66780.36841410.27356048618999
3.6678-3.77550.31221420.26885997613998
3.7755-3.89710.28921420.23966042618499
3.8971-4.03610.26311430.24276074621799
4.0361-4.19730.27491340.23426057619199
4.1973-4.38770.23871400.22136053619399
4.3877-4.61830.21851410.19816056619799
4.6183-4.90640.26551410.1966081622299
4.9064-5.28340.2351330.2046117625099
5.2834-5.81150.2841440.239261036247100
5.8115-6.64440.27961360.253161396275100
6.6444-8.34090.26911350.222261126247100
8.3409-29.87170.21881380.22636002614097
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)
10.7385-0.29030.37170.7432-0.46741.3030.08420.0003-0.0261-0.0779-0.00620.56430.1101-0.6475-00.7447-0.17860.03820.87630.01311.235832.922687.418193.7297
20.47440.37360.31280.67110.2460.98270.0034-0.23910.18420.1562-0.11590.5570.1728-0.7026-0.05190.8464-0.32730.21360.9099-0.00431.146135.54783.9542110.9342
30.84170.04140.35441.4002-0.08550.89610.1025-0.21270.24770.3767-0.10430.2245-0.2151-0.4642-0.03870.9566-0.16780.21710.6373-0.00950.970749.550595.6846116.0338
41.38660.2894-0.15830.946-0.28021.8710.0967-0.0160.2030.13840.02670.0391-0.2428-0.1349-0.0070.847-0.13850.05090.3418-0.00440.74568.3328104.383793.5497
51.0036-0.73860.38560.99480.42671.21620.0277-0.10720.1028-0.1847-0.03690.1784-0.2003-0.1603-0.00220.8994-0.0876-0.03850.4125-0.00370.884162.546289.185577.6415
60.84240.00860.24451.613-0.10661.67110.1050.1365-0.086-0.4965-0.0680.46720.0683-0.16590.02090.8267-0.1203-0.12080.39750.01860.881956.174887.204973.6295
70.2734-0.05020.09770.250.21550.21930.0977-0.53841.01410.4739-0.30070.0271-0.74220.1341-0.01111.4705-0.50990.1121.036-0.00861.244663.325976.2264136.5706
80.99870.367-0.10921.32880.10990.52130.3327-0.6194-0.14780.8563-0.2461-0.0280.1053-0.07390.94741.6681-0.65520.07090.97980.0640.791667.489564.456161.93
90.0029-0.00460.00360.0074-0.00210.0044-0.0684-0.1965-0.29690.0248-0.11630.16430.0634-0.2274-0.00012.0134-0.64580.08921.4025-0.11250.73568.200970.6513167.0221
100.0241-0.01960.02110.0236-0.01340.07420.01110.2691-0.15780.2715-0.12770.1250.0417-0.2382-0.00031.21-0.4340.02620.68440.02720.823466.138463.661145.9768
110.74390.2946-0.21340.706-0.46750.46460.1877-0.3178-0.0620.4072-0.1092-0.05280.36810.0310.68181.4413-0.6531-0.01710.75040.23140.926464.074843.9847150.7454
120.55450.75390.22891.01430.41070.53780.1723-0.4851-0.14330.1165-0.1558-0.2930.4350.0850.4572.2095-0.80460.52351.86820.11951.119544.840160.0146181.911
130.20220.1223-0.17760.0809-0.11420.1876-0.1936-0.3288-0.10660.2409-0.01810.1240.01510.0614-0.16682.6402-0.69150.58921.872-0.0861.012746.366774.9024194.4292
140.24040.01870.04940.00040.01050.01790.3846-0.89880.15690.2676-0.02150.1345-0.1787-0.2126-0.19662.6872-0.90970.4741.9469-0.05970.85455.181373.6421193.1274
150.0773-0.0805-0.01370.15190.07410.0348-0.1662-0.27370.54890.68670.2955-0.10050.0141-0.0285-0.00012.6219-0.56620.22031.8992-0.28781.184563.927687.3492200.9066
160.5111-1.1218-0.112.47720.25170.0289-0.1516-0.3327-0.0081.15940.1769-0.07890.02280.01150.01452.5828-0.87880.28311.76440.16910.932859.279166.3859192.8053
170.0386-0.16260.12840.7358-0.59540.4923-0.1166-0.1999-0.2150.5576-0.2121-0.15730.23180.19740.19212.6562-1.08540.2222.21730.48121.286452.453147.1963199.879
180.1336-0.07810.12970.0291-0.05090.10410.1559-0.7172-0.02980.5099-0.03280.0789-0.246-0.2827-0.46992.5991-0.90420.72482.01560.17011.011246.166962.4617198.9855
190.3782-0.32880.13620.2944-0.11940.5089-0.0274-0.388-0.07430.13090.25140.2582-0.2612-0.3156-0.05762.4033-0.83960.63211.54080.11850.852847.28469.4488188.27
200.3806-0.2687-0.27450.22910.07770.640.3347-0.3776-0.05850.5341-0.21440.2345-0.2594-0.4279-0.30881.3818-0.52180.41060.9505-0.02050.779744.615275.5051154.0175
210.64010.35320.84541.0450.42871.69650.08450.06530.1818-0.24070.26070.44630.0002-0.5077-0.10261.0795-0.52210.06310.89080.060.981147.38863.7491116.5897
220.6537-0.4681-0.36610.46660.3060.2474-0.1489-0.01030.6561-0.30650.5183-0.4199-0.26360.37940.2780.8573-0.4174-0.26531.0017-0.06661.1428116.792482.6936119.8155
230.7694-0.48090.07020.9429-0.07510.92560.0498-0.2257-0.20690.5692-0.067-0.42510.70190.45190.1261.6914-0.5174-0.49311.10110.07361.1476108.425367.957151.7587
240.9132-0.40930.00790.1679-0.0061-0.0203-0.1105-0.1016-0.38670.20920.05330.0777-0.17440.08910.05351.0093-0.2483-0.15960.62520.23120.776382.40542.4938191.0219
250.3318-0.2986-0.22640.28090.34040.8372-0.0431-0.3368-0.47020.2799-0.0949-0.0190.8261-0.1156-0.32381.3165-0.54860.10990.68550.06660.97857.22143.5147125.9131
260.20240.0148-0.07030.8754-0.62672.70760.2016-0.2065-0.32640.5234-0.22490.5783-0.0276-0.7071-0.28461.0928-0.4660.15670.74950.04740.970850.05557.0655124.2055
271.67480.8272-0.20960.402-0.09650.0115-0.16740.1203-0.5238-0.1211-0.19120.38130.2561-0.094-1.3791.1299-1.01730.14530.82510.13711.002551.324544.1712121.259
280.3446-0.1678-0.06410.26940.0121.18320.0493-0.1943-0.04130.2157-0.171-0.20330.3830.36650.01151.2763-0.2303-0.04920.61160.14010.917278.23543.4903119.1825
291.768-0.48750.16040.52550.18460.56030.2578-0.8250.57140.4056-0.02510.1556-0.06810.0206-0.07811.1137-0.40690.1990.80960.04821.05150.248871.3267125.907
300.67750.0692-0.20480.7984-0.2180.18510.0826-0.1732-0.22640.49060.01960.12310.0849-0.27750.4221.6877-0.88020.32511.08350.18111.012746.532944.9727158.1881
310.1101-0.07710.01760.0618-0.03810.0496-0.2848-0.0108-0.2913-0.021-0.0045-0.0076-0.0693-0.1110.00032.5282-0.91870.64082.26850.00611.588232.882253.9318196.6137
320.02040.0045-0.02520.06530.01470.0319-0.0862-0.0856-0.18080.1556-0.20850.1416-0.0970.107-0.00012.3691-0.65440.27831.93870.34981.582339.640435.218193.2179
330.52450.25310.07920.18060.1680.2712-0.1169-0.69190.02570.20420.0595-0.37110.0098-0.09-0.02662.3423-0.67630.49681.93970.29551.410742.67445.5501191.1534
340.1859-0.10350.0530.09490.03780.02560.5387-0.1345-1.10330.6642-0.00620.96270.9964-0.99710.03141.6723-0.19840.09551.0298-0.00971.478555.953584.670291.5292
350.1606-0.0868-0.03790.45840.19430.12060.4497-0.28950.39320.4306-0.01540.7756-0.2504-1.03970.00011.6709-0.28980.49411.3875-0.10241.362838.880490.9807152.5543
362.609-0.27821.76060.0268-0.1821.1893-0.5388-0.24890.42550.5197-0.03950.1523-0.611-0.1311-0.23882.3663-0.66790.57321.7939-0.08731.214337.844684.75186.336
370.0198-0.01540.00380.0075-0.0011-0.0001-0.0052-0.2705-0.49090.1701-0.3214-0.5526-0.10210.41480.00012.2944-0.33220.03541.1119-0.21851.470468.6174112.6449130.7576
380.33420.07830.02430.07680.11190.15290.2355-0.2046-0.06930.4277-0.27410.4254-0.4616-0.2755-0.00021.7946-0.2810.30211.0922-0.1571.129153.7098104.8043141.9631
390.0138-0.0083-0.02040.00180.01010.0193-0.2137-0.3040.37790.06320.41620.1757-0.0326-0.28360.00022.3277-0.30630.2611.7612-0.27921.438744.3713101.8033166.7921
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 215 )A1 - 215
2X-RAY DIFFRACTION2chain 'A' and (resid 216 through 264 )A216 - 264
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 446 )A265 - 446
4X-RAY DIFFRACTION4chain 'B' and (resid 15 through 223 )B15 - 223
5X-RAY DIFFRACTION5chain 'B' and (resid 224 through 293 )B224 - 293
6X-RAY DIFFRACTION6chain 'B' and (resid 294 through 439 )B294 - 439
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 32 )C2 - 32
8X-RAY DIFFRACTION8chain 'C' and (resid 33 through 286 or resid 1101 )C33 - 286
9X-RAY DIFFRACTION8chain 'C' and (resid 33 through 286 or resid 1101 )C1101
10X-RAY DIFFRACTION9chain 'C' and resid 1001C1001
11X-RAY DIFFRACTION10chain 'C' and resid 1002C1002
12X-RAY DIFFRACTION11chain 'C' and (resid 287 through 379 )C287 - 379
13X-RAY DIFFRACTION12chain 'D' and (resid 1 through 22 )D1 - 22
14X-RAY DIFFRACTION13chain 'D' and (resid 23 through 35 )D23 - 35
15X-RAY DIFFRACTION14chain 'D' and (resid 36 through 57 or resid 1001)D36 - 57
16X-RAY DIFFRACTION14chain 'D' and (resid 36 through 57 or resid 1001)D1001
17X-RAY DIFFRACTION15chain 'D' and (resid 58 through 84 )D58 - 84
18X-RAY DIFFRACTION16chain 'D' and (resid 85 through 131 )D85 - 131
19X-RAY DIFFRACTION17chain 'D' and (resid 132 through 151 )D132 - 151
20X-RAY DIFFRACTION18chain 'D' and (resid 152 through 178 )D152 - 178
21X-RAY DIFFRACTION19chain 'D' and (resid 179 through 197 )D179 - 197
22X-RAY DIFFRACTION20chain 'D' and (resid 198 through 231 )D198 - 231
23X-RAY DIFFRACTION21chain 'D' and (resid 232 through 241 )D232 - 241
24X-RAY DIFFRACTION22chain 'E' and (resid 1 through 15 )E1 - 15
25X-RAY DIFFRACTION23chain 'E' and (resid 16 through 73 )E16 - 73
26X-RAY DIFFRACTION24chain 'E' and (resid 74 through 196 or resid 1001)E74 - 196
27X-RAY DIFFRACTION24chain 'E' and (resid 74 through 196 or resid 1001)E1001
28X-RAY DIFFRACTION25chain 'F' and (resid 6 through 51 )F6 - 51
29X-RAY DIFFRACTION26chain 'F' and (resid 52 through 79 )F52 - 79
30X-RAY DIFFRACTION27chain 'F' and (resid 80 through 90 )F80 - 90
31X-RAY DIFFRACTION28chain 'F' and (resid 91 through 110 )F91 - 110
32X-RAY DIFFRACTION29chain 'G' and (resid 1 through 28 )G1 - 28
33X-RAY DIFFRACTION30chain 'G' and (resid 29 through 75 )G29 - 75
34X-RAY DIFFRACTION31chain 'H' and (resid 12 through 27 )H12 - 27
35X-RAY DIFFRACTION32chain 'H' and (resid 28 through 45 )H28 - 45
36X-RAY DIFFRACTION33chain 'H' and (resid 46 through 78 )H46 - 78
37X-RAY DIFFRACTION34chain 'I'I20 - 70
38X-RAY DIFFRACTION35chain 'J' and (resid 1 through 46 )J1 - 46
39X-RAY DIFFRACTION36chain 'J' and (resid 47 through 61 )J47 - 61
40X-RAY DIFFRACTION37chain 'K' and (resid 2 through 7 )K2 - 7
41X-RAY DIFFRACTION38chain 'K' and (resid 8 through 36 )K8 - 36
42X-RAY DIFFRACTION39chain 'K' and (resid 37 through 53 )K37 - 53

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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