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- PDB-5kli: Rhodobacter sphaeroides bc1 with stigmatellin and antimycin -

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データを開く


IDまたはキーワード:

読み込み中...

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基本情報

登録情報
データベース: PDB / ID: 5kli
タイトルRhodobacter sphaeroides bc1 with stigmatellin and antimycin
要素
  • Cytochrome b
  • Cytochrome c1
  • Ubiquinol-cytochrome c reductase iron-sulfur subunit
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


respiratory chain complex III / quinol-cytochrome-c reductase / quinol-cytochrome-c reductase activity / respiratory electron transport chain / 2 iron, 2 sulfur cluster binding / electron transfer activity / heme binding / metal ion binding / plasma membrane
類似検索 - 分子機能
Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b ...Ubiquitinol-cytochrome C reductase, Fe-S subunit, TAT signal / Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal / Single helix bin / Cytochrome c1, transmembrane anchor, C-terminal / Cytochrome Bc1 Complex; Chain C / Cytochrome Bc1 Complex; Chain C / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Cytochrome b / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / 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. / 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 / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
類似検索 - ドメイン・相同性
Chem-ANJ / FE2/S2 (INORGANIC) CLUSTER / HEME C / PROTOPORPHYRIN IX CONTAINING FE / Chem-LOP / STIGMATELLIN A / STRONTIUM ION / Cytochrome c1 / Cytochrome b / Ubiquinol-cytochrome c reductase iron-sulfur subunit
類似検索 - 構成要素
生物種Rhodobacter sphaeroides (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: 2.996 Å
データ登録者Xia, D. / Esser, L. / Zhou, F. / Tang, W.K. / Yu, C.A.
引用ジャーナル: J.Biol.Chem. / 年: 2016
タイトル: Hydrogen Bonding to the Substrate Is Not Required for Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III.
著者: Esser, L. / Zhou, F. / Zhou, Y. / Xiao, Y. / Tang, W.K. / Yu, C.A. / Qin, Z. / Xia, D.
履歴
登録2016年6月24日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02016年10月12日Provider: repository / タイプ: Initial release
改定 1.12016年11月2日Group: Database references
改定 1.22016年12月7日Group: Database references
改定 1.32023年9月27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 / citation / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _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6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

ダウンロードとリンク

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集合体

登録構造単位
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
E: Cytochrome b
F: Cytochrome c1
G: Ubiquinol-cytochrome c reductase iron-sulfur subunit
K: Cytochrome b
L: Cytochrome c1
M: Ubiquinol-cytochrome c reductase iron-sulfur subunit
O: Cytochrome b
P: Cytochrome c1
Q: Ubiquinol-cytochrome c reductase iron-sulfur subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)413,95546
ポリマ－398,42012
非ポリマー15,53634
水00
1
A: Cytochrome b
B: Cytochrome c1
C: Ubiquinol-cytochrome c reductase iron-sulfur subunit
E: Cytochrome b
F: Cytochrome c1
G: Ubiquinol-cytochrome c reductase iron-sulfur subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,97823
ポリマ－199,2106
非ポリマー7,76817
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area34810 Å2
ΔGint-421 kcal/mol
Surface area71020 Å2
手法PISA
2
K: Cytochrome b
L: Cytochrome c1
M: Ubiquinol-cytochrome c reductase iron-sulfur subunit
O: Cytochrome b
P: Cytochrome c1
Q: Ubiquinol-cytochrome c reductase iron-sulfur subunit
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)206,97823
ポリマ－199,2106
非ポリマー7,76817
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area34950 Å2
ΔGint-421 kcal/mol
Surface area70830 Å2
手法PISA
単位格子
Length a, b, c (Å)118.861, 126.929, 127.891
Angle α, β, γ (deg.)64.64, 87.69, 61.80
Int Tables number1
Space group name H-MP1

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要素

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タンパク質 , 3種, 12分子 AEKOBFLPCGMQ

#1: タンパク質
Cytochrome b


分子量: 50087.422 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Rhodobacter sphaeroides (バクテリア)
遺伝子: petB, fbcB / 発現宿主: Rhodobacter sp. (バクテリア) / 参照: UniProt: Q02761
#2: タンパク質
Cytochrome c1


分子量: 29589.158 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Rhodobacter sphaeroides (バクテリア)
遺伝子: petC, fbcC / 発現宿主: Rhodobacter sp. (バクテリア) / 参照: UniProt: Q02760
#3: タンパク質
Ubiquinol-cytochrome c reductase iron-sulfur subunit / Rieske iron-sulfur protein / RISP


分子量: 19928.375 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Rhodobacter sphaeroides (バクテリア)
遺伝子: petA, fbcF / 発現宿主: Rhodobacter sp. (バクテリア) / 参照: UniProt: Q02762, quinol-cytochrome-c reductase

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非ポリマー , 7種, 34分子

#4: 化合物
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


分子量: 616.487 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C34H32FeN4O4
#5: 化合物
ChemComp-SMA / STIGMATELLIN A


分子量: 514.650 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C30H42O7
#6: 化合物
ChemComp-ANJ / (2R,3S,6S,7R,8R)-3-{[3-(FORMYLAMINO)-2-HYDROXYBENZOYL]AMINO}-8-HEXYL-2,6-DIMETHYL-4,9-DIOXO-1,5-DIOXONAN-7-YL (2S)-2-METHYLBUTANOATE


分子量: 548.625 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C28H40N2O9
#7: 化合物
ChemComp-SR / STRONTIUM ION / ストロンチウムジカチオン


分子量: 87.620 Da / 分子数: 6 / 由来タイプ: 合成 / 式: Sr
#8: 化合物
ChemComp-LOP / (1R)-2-{[(R)-(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(DODECANOYLOXY)METHYL]ETHYL (9Z)-OCTADEC-9-ENOATE / LAURYL OLEYL PHOSPHATIDYL ETHANOLAMINE


分子量: 661.890 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C35H68NO8P / コメント: リン脂質*YM
#9: 化合物
ChemComp-HEC / HEME C


分子量: 618.503 Da / 分子数: 4 / 由来タイプ: 合成 / 式: C34H34FeN4O4
#10: 化合物
ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


分子量: 175.820 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Fe2S2

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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: 3.78 Å3/Da / 溶媒含有率: 67.43 %
結晶化温度: 289 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 8
詳細: 9% PEG400, 10 mM Sr(NO3)2, 0.06% sucrose mono caprate, 200 mM histidine, 150 mM NaCl, stigmatellin, antimycin

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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: 22-ID / 波長: 1 Å
検出器タイプ: MAR CCD 165 mm / 検出器: CCD / 日付: 2005年8月21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: 1 Å / 相対比: 1
反射解像度: 2.996→50 Å / Num. obs: 112899 / % possible obs: 92.7 % / 冗長度: 2.5 % / Rsym value: 0.078 / Net I/σ(I): 6.04
反射 シェル解像度: 2.996→3.07 Å / 冗長度: 1.8 % / Rmerge(I) obs: 0.492 / Rpim(I) all: 0.464

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.11rc1_2513: ???)精密化
HKL-2000データ収集
SCALEPACKデータスケーリング
MOLREP位相決定
PDB_EXTRACT3.2データ抽出
DENZOデータ削減
MOLREP位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2qjy

2qjy


解像度: 2.996→37.744 Å / SU ML: 0.39 / 交差検証法: FREE R-VALUE / σ(F): 0.94 / 位相誤差: 28.97 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2434 2030 1.8 %
Rwork0.2113 --
obs0.2119 112735 96.24 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
精密化ステップサイクル: LAST / 解像度: 2.996→37.744 Å
タンパク質核酸リガンド溶媒全体
原子数26916 0 1022 0 27938
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00828964
X-RAY DIFFRACTIONf_angle_d1.09339684
X-RAY DIFFRACTIONf_dihedral_angle_d13.96816356
X-RAY DIFFRACTIONf_chiral_restr0.0594180
X-RAY DIFFRACTIONf_plane_restr0.0074984
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9958-3.07070.37041180.33126573X-RAY DIFFRACTION80
3.0707-3.15370.40351370.32527710X-RAY DIFFRACTION94
3.1537-3.24640.34441500.30847862X-RAY DIFFRACTION95
3.2464-3.35120.30541410.28057928X-RAY DIFFRACTION97
3.3512-3.47090.30421430.25637957X-RAY DIFFRACTION97
3.4709-3.60970.31061590.23888057X-RAY DIFFRACTION98
3.6097-3.77390.21141500.22448029X-RAY DIFFRACTION98
3.7739-3.97260.25691410.20178062X-RAY DIFFRACTION98
3.9726-4.22120.2341580.19378075X-RAY DIFFRACTION98
4.2212-4.54670.18281440.17998065X-RAY DIFFRACTION98
4.5467-5.00330.21681430.17768071X-RAY DIFFRACTION99
5.0033-5.72510.23371480.18278140X-RAY DIFFRACTION99
5.7251-7.20480.22721540.19968132X-RAY DIFFRACTION99
7.2048-37.74710.1911440.17568044X-RAY DIFFRACTION98
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)
11.48971.1035-2.22920.8033-1.61763.3074-0.45520.4613-0.6196-0.66370.44790.30810.5436-1.8868-0.02571.1744-0.4508-0.29241.32490.33211.0825-32.0683-43.618310.9847
20.98750.5847-0.09641.018-0.38930.86590.4892-0.1691-0.2095-0.20120.55360.39990.7648-1.33251.94980.8324-0.6259-0.89341.19630.4090.8876-22.7562-48.084433.1459
30.1768-0.1023-0.32910.844-0.21270.74250.1233-0.0743-0.01940.18490.3160.12530.3948-0.4546-0.39130.9277-0.2659-0.39630.72870.22910.8719-7.672-43.464640.9372
41.14660.46870.15330.59530.43760.50280.1083-0.2586-0.0761-0.28650.13280.10740.9291-0.5548-0.20611.2026-0.3605-0.44590.73050.2440.8783-2.2725-58.518735.5228
50.2937-0.2464-0.53510.65560.1260.83280.1196-0.0763-0.1175-0.24030.11710.24040.527-0.7017-0.04771.152-0.4995-0.56930.89330.33720.943-14.3445-58.854737.2338
60.7011-0.6771-0.56640.66180.5440.4553-0.35450.1524-0.1405-0.17660.52940.40760.3122-0.5744-0.08381.2802-0.5781-0.45441.07180.45330.9123-20.1694-68.203748.241
71.96410.17970.74171.8584-0.06730.777-0.0307-0.43490.04410.19620.04730.38350.6245-0.8901-0.26181.3336-0.6381-0.51070.99460.371.0006-21.998-72.08843.922
82.2273-0.23440.03090.4570.1141.79510.0526-0.0832-0.0408-0.09890.18590.2311-0.2376-0.5513-0.24690.72270.0089-0.24680.70370.10660.7508-2.181-31.630164.0351
91.43961.40350.33591.40920.33390.0810.2865-0.22850.3951-0.8402-0.10280.5711-0.3954-0.4329-0.07590.96240.0962-0.26580.71050.14680.767-1.6012-20.267355.0314
103.08320.3501-0.05313.0446-0.20312.79710.00440.244-0.147-0.28080.217-0.391-0.13890.3571-0.31191.0863-0.0765-0.23960.64370.04240.854713.0882-18.690152.5786
111.77990.49680.14391.16360.01291.2085-0.0772-0.2052-0.01480.22220.16970.058-0.0063-0.3812-0.08010.8006-0.1259-0.26580.81510.15150.6749-3.3201-40.162162.8896
121.34860.1279-0.30721.1251-0.12231.1106-0.1035-0.42850.2044-0.01820.09970.1003-0.1641-0.1836-0.00440.92510.0029-0.25930.74530.08450.79880.0297-10.44330.8142
132.8344-0.59261.50491.8188-0.74782.4470.1694-0.40791.0797-0.15890.0368-0.0303-0.38450.1607-0.32331.4209-0.1451-0.16870.67720.08821.102311.27138.415627.9924
141.6972-0.3705-2.27983.07133.08115.3117-0.1483-0.54820.53920.51110.357-0.8937-0.96440.53570.56520.98-0.0358-0.57510.44980.10991.098614.4213-2.099329.1393
150.9617-0.82260.97931.76460.1471.92890.2824-0.00620.72770.4734-0.5907-0.774-0.35540.75420.30670.6732-0.0983-0.11570.44610.10830.740411.7831-8.674716.6354
162.22480.5027-0.16691.8994-1.11410.6601-0.3036-0.409-0.3863-0.44280.6304-1.3184-0.0533-0.1911-0.14160.9994-0.0485-0.19750.54370.11070.860811.0861-1.422717.3412
170.8344-0.25560.52441.24690.37390.99090.18270.0065-0.1708-0.2999-0.00440.3482-0.0198-0.2141-0.17840.9415-0.0501-0.22880.54980.21490.88445.1997-2.922416.7601
182.4148-0.61472.06391.21880.02675.99810.5351-0.5073-0.33260.44230.4809-0.94870.08530.0269-0.87631.23210.0655-0.25520.9481-0.0471.039514.6395-0.442738.9789
191.65710.59-0.111.3153-0.25922.6231-0.36090.48470.1638-0.319-0.383-0.4190.7195-0.75490.79081.6234-0.4859-0.49461.17710.33561.153-20.2962-63.44647.5595
200.3755-0.18110.10670.831-0.19870.78230.04490.24990.0498-0.7278-0.04690.11070.7681-0.08120.08251.2307-0.2167-0.46050.64570.15750.8799-3.0488-46.37134.3236
210.9050.852-0.3990.847-0.68231.3057-0.10880.03340.1459-0.3208-0.018-0.03660.0819-0.11470.10260.87-0.0644-0.29370.50260.12240.80438.0679-38.562815.473
220.9745-0.61810.20411.5372-0.15340.7036-0.09370.15810.0361-0.2040.32950.18040.1634-0.2434-0.21780.6755-0.1262-0.13050.56920.17070.6577-3.5737-26.507816.4066
230.4013-0.5837-0.10871.5207-0.17270.98510.02870.12730.0825-0.55440.06340.15570.288-0.2367-0.02710.8778-0.1854-0.26050.57280.16930.6769-4.2579-32.21095.5739
243.7625-1.58192.34934.1414-2.16396.98190.49050.3277-0.4816-1.21940.22550.56991.1803-0.8102-0.03450.8076-0.0394-0.0230.32470.00530.161-1.4659-24.0237-7.3977
251.06620.6083-0.02190.84990.33461.46350.13840.2903-0.0126-0.60730.10180.22360.4223-0.3615-0.23311.0853-0.0748-0.35680.59530.19930.7945-7.2932-23.9812-8.7538
261.61971.2147-0.10871.13060.3042.3970.05440.1113-0.0353-0.82770.17250.07560.3272-0.2637-0.24560.85980.16950.02350.56590.09961.077935.3364-36.665711.5535
273.69721.15980.37711.1190.51440.6897-0.7963-0.72240.1883-0.24110.1830.16480.2160.44370.53530.86070.0318-0.09970.50310.13180.817331.7311-31.766926.6735
281.2243-0.40450.342.7828-0.99811.98420.0971-0.1543-0.2318-0.0748-0.2435-0.30170.29030.24840.13580.811-0.1103-0.2170.66110.14371.050331.6064-38.737630.8532
290.6412-0.2928-0.08030.4173-0.03140.30320.14660.34260.15420.31360.10130.24550.7193-0.1055-0.13921.8502-0.053-0.29491.25640.33751.574521.5098-27.85080.9236
302.8741-2.0158-0.21021.7461-0.94863.6926-0.49560.45110.5654-0.7196-0.0621-1.2410.3510.77180.43440.52760.13350.26160.73540.10920.755837.6605-21.578611.0855
311.24560.32260.27462.4204-0.12621.6039-0.04480.13710.34010.3798-0.17050.0207-0.49610.57830.15431.0026-0.03310.08870.74350.21691.470835.4531-10.121814.3969
320.6303-0.11850.51610.47660.26011.49310.30410.0990.107-0.0231-0.3196-0.33770.49420.06790.00550.89110.0863-0.02450.52030.12790.948626.7437-36.75997.6467
330.3923-0.1277-0.020.2881-0.04021.00620.1776-0.0314-0.1266-0.206-0.1688-0.28680.2930.163-0.0091.1323-0.1105-0.26190.70250.19711.107518.9189-62.890138.5543
341.50340.71670.25221.34361.51931.99370.2034-0.1043-0.02750.1880.6962-0.07470.31630.0566-0.58761.2471-0.0654-0.40510.76820.37941.29528.5875-71.914556.41
350.999-0.2114-0.12030.17820.49931.7470.1515-0.3646-0.22320.12120.5089-0.91590.3030.5589-0.58370.9828-0.2477-0.55880.70150.09621.198924.2227-61.938454.3252
361.0881-0.16640.53390.8444-0.11310.71950.5538-0.0892-0.20520.6065-0.2662-0.32340.47220.3347-0.15331.1366-0.2418-0.49160.67680.23510.94749.9198-63.210655.1135
370.824-0.3254-0.95050.75150.85121.5126-0.6394-0.477-0.23040.09150.2893-0.4165-0.2108-0.48890.26760.9446-0.1359-0.26450.690.34690.866714.3222-68.75657.1037
381.6403-0.1416-0.0791.11290.38620.9278-0.03550.03390.5247-0.1846-0.0048-0.32320.34150.26670.09811.1551-0.2164-0.32930.66860.37930.991712.0463-71.095651.9412
391.64111.0216-0.29563.79291.02664.8853-0.2409-0.3260.4351-0.12160.9188-0.42330.27950.204-0.71640.9997-0.073-0.2720.65650.09981.211933.2121-59.244150.9738
400.563-0.15910.05482.2882-2.2632.5114-0.38280.2152-0.60320.41730.96670.21580.1147-1.4309-0.55981.0519-0.3141-0.16141.09340.19640.7977-32.740634.6835-46.2807
410.486-0.74171.20773.2453-1.09533.26150.3068-0.4239-0.1767-0.23220.2550.77150.367-0.69661.19720.3506-0.05520.01950.2861-0.07130.0432-23.748531.5512-23.7176
420.93850.5145-0.10812.9806-1.1451.4947-0.1931-0.18250.24190.36080.0414-0.2564-0.2484-0.0280.12070.44090.0128-0.0670.33550.00690.3642-9.110537.3-15.9584
431.899-0.76321.83260.8498-0.36042.55890.3629-0.2325-0.5516-0.4027-0.0819-0.06390.7086-0.32260.22880.38880.09070.17430.2425-0.08410.2057-2.654722.467-20.4827
441.8094-0.24540.20922.0103-0.28270.99590.1282-0.0364-0.4136-0.24570.12960.18830.4541-0.2757-0.26370.5177-0.0807-0.01720.44030.05170.2992-14.816921.5584-19.0506
452.21870.37530.61144.4048-2.13283.7373-0.2729-0.20380.0247-0.48060.32050.33150.0982-0.4738-0.3040.5076-0.0330.00730.49130.06190.5203-20.305812.0807-7.951
461.47390.02660.14710.422-0.21741.24090.105-0.3139-0.4394-0.21840.02410.35050.5577-0.4982-0.10620.7496-0.1906-0.19060.50670.15020.696-21.94998.0076-12.1332
472.66-0.65460.55342.3215-0.6753.30760.1012-0.2383-1.13120.53910.2709-0.171-0.0083-0.493-0.2540.81490.0853-0.16440.73710.02441.1197-12.834744.63598.3971
481.3573-0.453-0.22671.64520.86433.12490.28150.17420.1031-0.2717-0.1444-0.4429-0.3632-0.1469-0.07660.7002-0.0083-0.20570.45360.02040.73331.200455.27235.3198
493.39111.06040.44221.5021-0.71090.71830.04340.03941.1513-0.6410.12360.81080.1668-0.3621-0.1420.80330.0996-0.25520.58910.11011.007-4.995661.4686-3.0327
501.3776-0.35080.22752.1210.13031.6973-0.03840.11420.1549-0.07290.07740.04-0.1712-0.13180.01480.8928-0.0432-0.3040.66780.04930.82542.758650.3688-0.9709
511.67160.2736-0.42822.51210.44322.9806-0.0805-0.58420.23131.06380.1166-0.1703-0.1780.2705-0.32420.48320.01620.04230.3582-0.37030.2752-0.210641.115517.0142
521.38420.0661-0.61642.2938-0.33431.1538-0.1304-0.4241-0.20370.67250.0345-0.07030.2450.20520.04670.90380.0026-0.2920.6760.04580.69135.434438.261918.4017
534.74461.69873.60651.64461.51212.6897-0.53170.41250.7039-0.12120.11880.0964-0.4620.13910.30710.5580.0435-0.10050.63320.01130.4858-23.135645.1901-6.8107
541.18130.8025-0.23830.8061-0.46131.0452-0.22380.06940.382-0.15090.13090.2848-0.2781-0.01020.06090.9593-0.0627-0.28690.70520.13070.9268-3.176370.1164-27.2226
553.76810.50051.08891.2690.39971.08790.2276-0.4160.6763-0.6220.066-0.08920.1866-0.1071-0.33681.2409-0.2767-0.45610.82760.28141.25017.009389.4129-30.6432
560.40370.1607-0.39560.2742-0.38690.7086-0.3868-0.63190.59650.72550.1938-0.432-0.48380.2572-0.01140.952-0.1567-0.42510.76940.13520.923210.701779.0503-29.0185
570.72410.2660.1070.6022-0.32250.4004-0.01670.34520.55290.4336-0.1473-0.0092-0.46610.47750.17360.9764-0.2076-0.32940.69970.28610.93849.073971.9362-41.3738
583.61271.00410.05732.5907-1.49661.8686-0.5499-0.0066-0.32450.02250.3246-0.5768-0.722-0.26180.18021.0125-0.1626-0.2640.70540.20920.84247.923379.1866-40.995
590.61190.04610.97940.68480.50021.8241-0.07980.13660.33430.12920.30880.12560.23680.1232-0.21841.0164-0.1406-0.17370.65540.27780.78862.195177.3133-41.7451
600.8749-0.4501-1.53353.1061-0.48493.32150.4437-0.5302-0.16110.28580.4906-0.18770.00530.6405-0.92451.2649-0.1466-0.30420.90480.1121.038110.385881.1031-19.1816
611.65531.0958-1.07561.42190.2952.3933-0.13720.8563-0.1559-0.8350.06110.10150.2819-1.21970.10071.1524-0.2925-0.19491.04120.0830.778-19.701515.2106-48.5492
622.14831.53061.96314.806-0.07853.2112-0.40250.77560.1191-1.53130.55730.27150.3590.1992-0.01870.3884-0.16120.00240.50020.00320.2303-3.263832.9106-52.1991
631.5423-1.01531.39492.0795-1.21371.3714-0.37620.46180.5754-0.2047-0.1361-0.85360.13880.24320.48510.5291-0.15410.05150.58870.08760.39927.161341.9124-41.2265
641.19040.13860.00850.97530.06360.8476-0.20310.3310.1106-0.46590.2580.1634-0.1967-0.0649-0.00890.7644-0.1514-0.19450.64620.17460.6786-5.28653.2605-41.2023
650.4865-0.70730.05441.6278-0.45390.7798-0.29160.29490.2959-0.3650.1380.193-0.0744-0.06820.12090.7671-0.2725-0.13070.71140.19070.576-5.253946.9829-51.7827
661.84940.5880.12142.10390.13731.04250.2492-0.0081-0.1502-0.6560.02010.19590.7377-1.141-0.24170.9734-0.3081-0.00320.82520.19960.5012-2.39454.6357-65.0563
671.03150.72780.12480.63430.51151.1504-0.1160.71630.1934-0.57010.34160.30560.1-0.0305-0.21191.074-0.2075-0.22490.84690.30780.7106-8.173354.3248-66.5445
681.84830.75350.07232.92020.37442.66710.20420.0493-0.1062-1.2947-0.47640.2095-0.00230.6180.28640.7926-0.03970.22540.74960.01471.074230.363446.2101-50.7736
690.9107-0.6101-0.2260.5058-0.06320.5278-0.38230.47180.38920.09110.0006-0.46940.27760.07340.12760.45720.06740.16270.76270.03321.049639.47943.7966-36.4784
701.83660.54420.35410.2120.03141.0492-0.1497-0.1776-0.1177-0.31080.09260.2524-0.15660.55050.02410.794-0.1235-0.02310.69420.18580.999131.262242.7695-31.1175
711.1340.2360.09761.5941-0.83722.2342-0.1307-0.2132-0.25060.3917-0.27410.0386-0.25730.12740.32690.738-0.212-0.23330.77430.21771.090731.130744.9432-20.2124
721.49430.27420.40371.0653-0.34630.6978-0.23840.69130.4093-1.1407-0.03130.41970.4596-0.00750.25871.0709-0.2406-0.08970.94510.18180.979124.423452.8646-48.4476
730.61640.7051-0.38392.515-1.55790.9671-0.07110.12430.5272-0.352-0.17450.2888-0.86440.55960.16551.1149-0.3166-0.06030.96920.32661.683536.844472.9167-44.4916
742.13540.92820.66261.5862-0.03592.720.70340.0957-0.1730.1482-0.40470.0694-0.16980.3938-0.29381.0839-0.02530.05050.72440.21691.276630.026967.6598-44.7691
751.2528-0.40110.75430.64770.71832.0235-0.18360.33040.3943-0.18470.0953-0.4686-0.02780.15350.11250.6956-0.15520.15660.74980.18860.807825.668144.409-48.9255
760.8907-0.56140.00680.8948-0.26421.1319-0.052-0.1524-0.20.02480.0169-0.57840.12030.0884-0.02030.6807-0.1112-0.04160.64550.15540.972818.580219.506-16.4775
772.56311.58071.67321.6951.65283.2387-0.0114-0.23260.04570.39060.1333-0.81280.52320.7123-0.16950.70380.1301-0.08890.85260.27611.113428.257512.0081.9848
784.9637-1.5671-1.22490.85821.2622.45430.1814-0.883-0.3606-0.16710.118-0.8612-0.0110.4843-0.3510.7353-0.2002-0.42650.52770.18281.376123.441121.6102-0.5954
794.39061.6126-0.36645.1074-0.83041.08910.1552-0.69160.11881.1013-0.5679-0.6963-0.29980.72570.30270.47350.0067-0.13030.44410.10910.50119.291919.3194-0.4087
802.5169-1.48780.28241.5658-0.29120.4834-0.6421-1.03670.028-0.19770.3834-0.2287-0.2034-0.7810.25190.50040.092-0.02890.6070.03980.630614.00714.1971.8836
811.1573-0.11640.51691.0010.09480.27560.14110.23140.03810.08350.1028-0.0180.63630.0115-0.1881.01050.0041-0.23360.59830.27620.933312.057111.5104-3.204
821.3418-0.3009-0.89891.6174-1.14011.8091-0.323-0.730.84850.03840.2491-0.8253-0.22380.31240.00920.6930.04070.03670.7840.08851.512932.368724.7663-3.6622
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 33 )
2X-RAY DIFFRACTION2chain 'A' and (resid 34 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 117 or resid 1001)
4X-RAY DIFFRACTION4chain 'A' and (resid 118 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 360 or resid 1002)
6X-RAY DIFFRACTION6chain 'A' and (resid 361 through 382 )
7X-RAY DIFFRACTION7chain 'A' and (resid 383 through 430 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 46 )
9X-RAY DIFFRACTION9chain 'B' and (resid 47 through 59 )
10X-RAY DIFFRACTION10chain 'B' and (resid 60 through 79 )
11X-RAY DIFFRACTION11chain 'B' and (resid 80 through 256 )
12X-RAY DIFFRACTION12chain 'C' and (resid 9 through 107 )
13X-RAY DIFFRACTION13chain 'C' and (resid 108 through 120 )
14X-RAY DIFFRACTION14chain 'C' and (resid 121 through 128 )
15X-RAY DIFFRACTION15chain 'C' and (resid 129 through 152 or resid 1001)
16X-RAY DIFFRACTION16chain 'C' and (resid 153 through 161 )
17X-RAY DIFFRACTION17chain 'C' and (resid 162 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 172 through 187 )
19X-RAY DIFFRACTION19chain 'E' and (resid 3 through 33 )
20X-RAY DIFFRACTION20chain 'E' and (resid 34 through 67 )
21X-RAY DIFFRACTION21chain 'E' and (resid 68 through 117 or resid 1001)
22X-RAY DIFFRACTION22chain 'E' and (resid 118 through 187 )
23X-RAY DIFFRACTION23chain 'E' and (resid 188 through 360 or resid 1002)
24X-RAY DIFFRACTION24chain 'E' and (resid 361 through 382 )
25X-RAY DIFFRACTION25chain 'E' and (resid 383 through 430 )
26X-RAY DIFFRACTION26chain 'F' and (resid 1 through 34 )
27X-RAY DIFFRACTION27chain 'F' and (resid 35 through 46 )
28X-RAY DIFFRACTION28chain 'F' and (resid 47 through 107 )
29X-RAY DIFFRACTION29chain 'F' and (resid 108 through 126 )
30X-RAY DIFFRACTION30chain 'F' and (resid 127 through 143 )
31X-RAY DIFFRACTION31chain 'F' and (resid 144 through 166 )
32X-RAY DIFFRACTION32chain 'F' and (resid 167 through 256 )
33X-RAY DIFFRACTION33chain 'G' and (resid 9 through 107 )
34X-RAY DIFFRACTION34chain 'G' and (resid 108 through 120 )
35X-RAY DIFFRACTION35chain 'G' and (resid 121 through 128 )
36X-RAY DIFFRACTION36chain 'G' and (resid 129 through 152 or resid 1001)
37X-RAY DIFFRACTION37chain 'G' and (resid 153 through 161 )
38X-RAY DIFFRACTION38chain 'G' and (resid 162 through 171 )
39X-RAY DIFFRACTION39chain 'G' and (resid 172 through 187 )
40X-RAY DIFFRACTION40chain 'K' and (resid 3 through 33 )
41X-RAY DIFFRACTION41chain 'K' and (resid 34 through 67 )
42X-RAY DIFFRACTION42chain 'K' and (resid 68 through 117 or resid 1001)
43X-RAY DIFFRACTION43chain 'K' and (resid 118 through 187 )
44X-RAY DIFFRACTION44chain 'K' and (resid 188 through 360 or resid 1002)
45X-RAY DIFFRACTION45chain 'K' and (resid 361 through 382 )
46X-RAY DIFFRACTION46chain 'K' and (resid 383 through 430 )
47X-RAY DIFFRACTION47chain 'L' and (resid 1 through 21 )
48X-RAY DIFFRACTION48chain 'L' and (resid 22 through 46 )
49X-RAY DIFFRACTION49chain 'L' and (resid 47 through 59 )
50X-RAY DIFFRACTION50chain 'L' and (resid 60 through 126 )
51X-RAY DIFFRACTION51chain 'L' and (resid 127 through 143 )
52X-RAY DIFFRACTION52chain 'L' and (resid 144 through 203 )
53X-RAY DIFFRACTION53chain 'L' and (resid 204 through 256 )
54X-RAY DIFFRACTION54chain 'M' and (resid 9 through 107 )
55X-RAY DIFFRACTION55chain 'M' and (resid 108 through 120 )
56X-RAY DIFFRACTION56chain 'M' and (resid 121 through 128 )
57X-RAY DIFFRACTION57chain 'M' and (resid 129 through 152 or resid 1001)
58X-RAY DIFFRACTION58chain 'M' and (resid 153 through 161 )
59X-RAY DIFFRACTION59chain 'M' and (resid 162 through 171 )
60X-RAY DIFFRACTION60chain 'M' and (resid 172 through 187 )
61X-RAY DIFFRACTION61chain 'O' and (resid 3 through 33 )
62X-RAY DIFFRACTION62chain 'O' and (resid 34 through 67 )
63X-RAY DIFFRACTION63chain 'O' and (resid 68 through 117 or resid 1001)
64X-RAY DIFFRACTION64chain 'O' and (resid 118 through 187 )
65X-RAY DIFFRACTION65chain 'O' and (resid 188 through 360 or resid 1002)
66X-RAY DIFFRACTION66chain 'O' and (resid 361 through 382 )
67X-RAY DIFFRACTION67chain 'O' and (resid 383 through 430 )
68X-RAY DIFFRACTION68chain 'P' and (resid 1 through 21 )
69X-RAY DIFFRACTION69chain 'P' and (resid 22 through 34 )
70X-RAY DIFFRACTION70chain 'P' and (resid 35 through 59 )
71X-RAY DIFFRACTION71chain 'P' and (resid 60 through 97 )
72X-RAY DIFFRACTION72chain 'P' and (resid 98 through 135 )
73X-RAY DIFFRACTION73chain 'P' and (resid 136 through 154 )
74X-RAY DIFFRACTION74chain 'P' and (resid 155 through 166 )
75X-RAY DIFFRACTION75chain 'P' and (resid 167 through 256 )
76X-RAY DIFFRACTION76chain 'Q' and (resid 9 through 107 )
77X-RAY DIFFRACTION77chain 'Q' and (resid 108 through 120 )
78X-RAY DIFFRACTION78chain 'Q' and (resid 121 through 128 )
79X-RAY DIFFRACTION79chain 'Q' and (resid 129 through 152 or resid 1001)
80X-RAY DIFFRACTION80chain 'Q' and (resid 153 through 161 )
81X-RAY DIFFRACTION81chain 'Q' and (resid 162 through 171 )
82X-RAY DIFFRACTION82chain 'Q' and (resid 172 through 187 )

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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