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- PDB-7k6c: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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基本情報

登録情報
データベース: PDB / ID: 7k6c
タイトルCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium abscessus ATCC 19977 / DSM 44196 with NADP and inhibitor P218
要素Dihydrofolate reductase
キーワードOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / SDDC / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
機能・相同性
機能・相同性情報


dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / metal ion binding
類似検索 - 分子機能
Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily
類似検索 - ドメイン・相同性
Chem-MMV / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
類似検索 - 構成要素
生物種Mycobacteroides abscessus (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 Å
データ登録者Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Santhakumar, V. / Walpole, C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
引用ジャーナル: J.Med.Chem. / 年: 2024
タイトル: Rational Exploration of 2,4-Diaminopyrimidines as DHFR Inhibitors Active against Mycobacterium abscessus and Mycobacterium avium , Two Emerging Human Pathogens.
著者: Andrade Meirelles, M. / Almeida, V.M. / Sullivan, J.R. / de Toledo, I. / Dos Reis, C.V. / Cunha, M.R. / Zigweid, R. / Shim, A. / Sankaran, B. / Woodward, E.L. / Seibold, S. / Liu, L. / Mian, ...著者: Andrade Meirelles, M. / Almeida, V.M. / Sullivan, J.R. / de Toledo, I. / Dos Reis, C.V. / Cunha, M.R. / Zigweid, R. / Shim, A. / Sankaran, B. / Woodward, E.L. / Seibold, S. / Liu, L. / Mian, M.R. / Battaile, K.P. / Riley, J. / Duncan, C. / Simeons, F.R.C. / Ferguson, L. / Joji, H. / Read, K.D. / Lovell, S. / Staker, B.L. / Behr, M.A. / Pilli, R.A. / Counago, R.M.
履歴
登録2020年9月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年3月17日Provider: repository / タイプ: Initial release
改定 1.12023年10月18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
改定 1.22024年11月13日Group: Database references / Structure summary
カテゴリ: audit_author / citation ...audit_author / citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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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: Dihydrofolate reductase
B: Dihydrofolate reductase
C: Dihydrofolate reductase
D: Dihydrofolate reductase
E: Dihydrofolate reductase
F: Dihydrofolate reductase
G: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)138,81031
ポリマ－130,5517
非ポリマー8,25924
水15,331851
1
A: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,7944
ポリマ－18,6501
非ポリマー1,1443
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
2
B: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8966
ポリマ－18,6501
非ポリマー1,2465
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
3
C: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8565
ポリマ－18,6501
非ポリマー1,2064
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
4
D: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8164
ポリマ－18,6501
非ポリマー1,1663
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
5
E: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8164
ポリマ－18,6501
非ポリマー1,1663
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
6
F: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8164
ポリマ－18,6501
非ポリマー1,1663
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
7
G: Dihydrofolate reductase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)19,8164
ポリマ－18,6501
非ポリマー1,1663
水181
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)75.630, 62.490, 124.550
Angle α, β, γ (deg.)90.000, 94.670, 90.000
Int Tables number4
Space group name H-MP1211
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
11(chain A and (resid 4 through 12 or resid 14...
21(chain B and (resid 4 through 12 or resid 14...
31(chain C and (resid 4 through 12 or resid 14...
41(chain D and (resid 4 through 12 or resid 14...
51(chain E and (resid 4 through 12 or resid 14...
61(chain F and (resid 4 through 12 or resid 14...
71(chain G and (resid 4 through 12 or resid 14...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 4 through 12 or resid 14...A4 - 12
121(chain A and (resid 4 through 12 or resid 14...A14 - 30
131(chain A and (resid 4 through 12 or resid 14...A32 - 35
141(chain A and (resid 4 through 12 or resid 14...A3 - 200
151(chain A and (resid 4 through 12 or resid 14...A3 - 200
161(chain A and (resid 4 through 12 or resid 14...A3 - 200
171(chain A and (resid 4 through 12 or resid 14...A3 - 200
181(chain A and (resid 4 through 12 or resid 14...A3 - 200
191(chain A and (resid 4 through 12 or resid 14...A3 - 200
211(chain B and (resid 4 through 12 or resid 14...B4 - 12
221(chain B and (resid 4 through 12 or resid 14...B14 - 19
231(chain B and (resid 4 through 12 or resid 14...B20
241(chain B and (resid 4 through 12 or resid 14...B3 - 200
251(chain B and (resid 4 through 12 or resid 14...B3 - 200
261(chain B and (resid 4 through 12 or resid 14...B3 - 200
271(chain B and (resid 4 through 12 or resid 14...B3 - 200
311(chain C and (resid 4 through 12 or resid 14...C4 - 12
321(chain C and (resid 4 through 12 or resid 14...C14 - 19
331(chain C and (resid 4 through 12 or resid 14...C20
341(chain C and (resid 4 through 12 or resid 14...C3 - 200
351(chain C and (resid 4 through 12 or resid 14...C3 - 200
361(chain C and (resid 4 through 12 or resid 14...C3 - 200
371(chain C and (resid 4 through 12 or resid 14...C3 - 200
411(chain D and (resid 4 through 12 or resid 14...D4 - 12
421(chain D and (resid 4 through 12 or resid 14...D14 - 19
431(chain D and (resid 4 through 12 or resid 14...D4 - 200
441(chain D and (resid 4 through 12 or resid 14...D4 - 200
451(chain D and (resid 4 through 12 or resid 14...D4 - 200
461(chain D and (resid 4 through 12 or resid 14...D4 - 200
471(chain D and (resid 4 through 12 or resid 14...D4 - 200
481(chain D and (resid 4 through 12 or resid 14...D4 - 200
511(chain E and (resid 4 through 12 or resid 14...E4 - 12
521(chain E and (resid 4 through 12 or resid 14...E14 - 19
531(chain E and (resid 4 through 12 or resid 14...E20
541(chain E and (resid 4 through 12 or resid 14...E3 - 200
551(chain E and (resid 4 through 12 or resid 14...E3 - 200
561(chain E and (resid 4 through 12 or resid 14...E3 - 200
571(chain E and (resid 4 through 12 or resid 14...E3 - 200
611(chain F and (resid 4 through 12 or resid 14...F4 - 12
621(chain F and (resid 4 through 12 or resid 14...F14 - 19
631(chain F and (resid 4 through 12 or resid 14...F20
641(chain F and (resid 4 through 12 or resid 14...F3 - 200
651(chain F and (resid 4 through 12 or resid 14...F3 - 200
661(chain F and (resid 4 through 12 or resid 14...F3 - 200
671(chain F and (resid 4 through 12 or resid 14...F3 - 200
711(chain G and (resid 4 through 12 or resid 14...G4 - 12
721(chain G and (resid 4 through 12 or resid 14...G14 - 19
731(chain G and (resid 4 through 12 or resid 14...G20
741(chain G and (resid 4 through 12 or resid 14...G3 - 200
751(chain G and (resid 4 through 12 or resid 14...G3 - 200
761(chain G and (resid 4 through 12 or resid 14...G3 - 200
771(chain G and (resid 4 through 12 or resid 14...G3 - 200

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要素

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タンパク質 , 1種, 7分子 ABCDEFG

#1: タンパク質
Dihydrofolate reductase


分子量: 18650.094 Da / 分子数: 7 / 変異: C84S, E141T / 由来タイプ: 組換発現
由来: (組換発現) Mycobacteroides abscessus (strain ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543) (バクテリア)
株: ATCC 19977 / DSM 44196 / CIP 104536 / JCM 13569 / NCTC 13031 / TMC 1543
遺伝子: MAB_3090c / プラスミド: MyabA.01062.a.B15 / 発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 株 (発現宿主): BL21(DE3) / 参照: UniProt: B1MD46, dihydrofolate reductase

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非ポリマー , 5種, 875分子

#2: 化合物
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


分子量: 743.405 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C21H28N7O17P3 / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物
ChemComp-MMV / 3-(2-{3-[(2,4-diamino-6-ethylpyrimidin-5-yl)oxy]propoxy}phenyl)propanoic acid / P-218


分子量: 360.408 Da / 分子数: 7 / 由来タイプ: 合成 / 式: C18H24N4O4 / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Ca
#5: 化合物
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / エチレングリコ-ル


分子量: 62.068 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C2H6O2
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 851 / 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: 2.23 Å3/Da / 溶媒含有率: 44.8 %
結晶化温度: 287 K / 手法: 蒸気拡散法, シッティングドロップ法 / pH: 6.5
詳細: Optimization screen based on Microlytics MCSG1 B6: 200mM CaOAc2, 20% (w/V) PEG 8000, 100mM MES / NaOH pH 6.5: MyabA.01062.a.B15.PS38597 at 12.39mg/ml + 3.5mM NADP + 3mM P218: tray 317391 F7: ...詳細: Optimization screen based on Microlytics MCSG1 B6: 200mM CaOAc2, 20% (w/V) PEG 8000, 100mM MES / NaOH pH 6.5: MyabA.01062.a.B15.PS38597 at 12.39mg/ml + 3.5mM NADP + 3mM P218: tray 317391 F7: cryo 20% EG + compounds: puck kdu7-5

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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: 21-ID-F / 波長: 0.97872 Å
検出器タイプ: RAYONIX MX-300 / 検出器: CCD / 日付: 2020年8月6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: 0.97872 Å / 相対比: 1
反射解像度: 2→37.69 Å / Num. obs: 78407 / % possible obs: 99.7 % / 冗長度: 3.737 % / Biso Wilson estimate: 31.922 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.084 / Χ2: 0.911 / Net I/σ(I): 13.87 / Num. measured all: 292968 / Scaling rejects: 6
反射 シェル

Diffraction-ID: 1

解像度 (Å)冗長度 (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.053.2830.5452.2418775575757180.760.65399.3
2.05-2.113.730.4922.9120977563156240.850.57599.9
2.11-2.173.7870.3743.7520693547254640.9140.43699.9
2.17-2.243.7860.314.5320205534753370.9310.36199.8
2.24-2.313.7850.2685.2919478515651460.9490.31299.8
2.31-2.393.7950.2246.218928499449880.9630.26199.9
2.39-2.483.7920.1957.0118246482348120.970.22799.8
2.48-2.583.7990.1538.717580463346280.9820.17899.9
2.58-2.73.7910.13110.0816895446744570.9860.15299.8
2.7-2.833.7960.10912.0216126425942480.990.12799.7
2.83-2.983.7910.08414.9515485409540850.9940.09899.8
2.98-3.163.7920.06418.7214507383238260.9960.07599.8
3.16-3.383.780.0522.9813590360235950.9970.05899.8
3.38-3.653.7760.04127.7512732338733720.9980.04899.6
3.65-43.760.03432.2511659311231010.9980.03999.6
4-4.473.7570.02837.2410596282628200.9990.03399.8
4.47-5.163.7520.02737.99332249524870.9990.03299.7
5.16-6.323.7210.0334.667929213621310.9990.03699.8
6.32-8.943.6770.02638.416071165716510.9990.0399.6
8.94-37.693.450.02343.731649449170.9990.02797.1

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解析

ソフトウェア
名称バージョン分類
XDSデータ削減
XSCALEデータスケーリング
PHENIX1.18.2精密化
PDB_EXTRACT3.25データ抽出
MoRDa位相決定
PHENIXモデル構築
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: PDB entry 2w3v as per MORDA

2w3v


解像度: 2→37.69 Å / SU ML: 0.21 / 交差検証法: THROUGHOUT / σ(F): 1.35 / 位相誤差: 20.57 / 立体化学のターゲット値: ML
Rfactor反射数%反射Selection details
Rfree0.2072 2082 2.66 %0
Rwork0.1655 76298 --
obs0.1666 78380 99.72 %-
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
原子変位パラメータBiso max: 88.19 Å2 / Biso mean: 30.7549 Å2 / Biso min: 10.79 Å2
精密化ステップサイクル: final / 解像度: 2→37.69 Å
タンパク質核酸リガンド溶媒全体
原子数8374 0 546 853 9773
Biso mean--27.1 35.24 -
残基数----1115
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.0079294
X-RAY DIFFRACTIONf_angle_d0.93112771
X-RAY DIFFRACTIONf_dihedral_angle_d15.6943467
X-RAY DIFFRACTIONf_chiral_restr0.0571389
X-RAY DIFFRACTIONf_plane_restr0.0081759
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-ID数Refine-IDRmsタイプ
11A4335X-RAY DIFFRACTION4.878TORSIONAL
12B4335X-RAY DIFFRACTION4.878TORSIONAL
13C4335X-RAY DIFFRACTION4.878TORSIONAL
14D4335X-RAY DIFFRACTION4.878TORSIONAL
15E4335X-RAY DIFFRACTION4.878TORSIONAL
16F4335X-RAY DIFFRACTION4.878TORSIONAL
17G4335X-RAY DIFFRACTION4.878TORSIONAL
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.050.24571460.21855017516399
2.05-2.10.29391330.215150495182100
2.1-2.150.26661410.206650685209100
2.15-2.220.22621280.193450475175100
2.22-2.290.25891480.190150815229100
2.29-2.370.2541350.185650305165100
2.37-2.470.22241270.187650835210100
2.47-2.580.25791190.180151075226100
2.58-2.710.22031640.185850825246100
2.71-2.880.21651340.173950635197100
2.88-3.110.21651420.170250735215100
3.11-3.420.21641470.163651125259100
3.42-3.910.1541410.143551225263100
3.91-4.930.15781510.123151115262100
4.93-37.690.20681260.15835253537999
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)
13.3229-1.035-0.13323.034-0.48780.10920.044-0.74010.0275-0.02990.32220.10940.0160.1938-0.1520.13780.04190.01160.65460.01340.24858.4322-2.874850.914
21.658-0.6003-0.01910.3975-0.35231.6354-0.0682-1.83060.4222-0.03830.29960.20730.0617-0.405-0.24470.2241-0.00230.1031.1448-0.01910.25843.6925-0.495358.6136
36.5442-3.0984-1.75394.45671.62733.1667-0.2213-1.7567-0.70070.9338-0.17330.91540.2860.3670.23590.2928-0.02650.05490.67040.13970.5-8.5721-5.788356.6692
40.9441-0.21330.07250.82090.06931.31920.012-0.7725-0.6180.12070.0408-0.09840.1582-0.1966-0.05930.2099-0.0369-0.03870.50230.19050.33740.2045-8.922547.8019
51.3398-0.7471-0.33081.8098-0.0653.33980.1726-1.0684-0.0383-0.04610.1654-0.23940.0555-0.214-0.11150.17090.0192-0.03020.6327-0.02050.212714.6829-3.773153.3677
62.2823-1.4281-3.77953.61791.10576.8106-0.2308-1.33730.82820.34780.1894-0.1877-0.556-0.0812-0.38990.33890.1004-0.02140.9488-0.43590.667717.579.726560.4736
72.3287-0.7009-1.04184.26740.61065.23730.2694-0.69990.8962-0.14850.1444-0.3421-0.54720.0951-0.84320.1890.04640.01170.4236-0.16770.337815.1383.021949.2643
84.23970.20450.15121.9242-1.33944.8941-0.04440.2147-0.0603-0.05470.0010.0606-0.12980.00520.04770.14930.0175-0.00820.0601-0.01730.1721-16.326-8.03710.691
97.2606-0.68154.65084.3121-2.08564.0466-0.162-0.11080.6934-0.0031-0.02370.2178-0.2889-0.12980.18130.1513-0.0172-0.00010.0872-0.00450.2366-11.16792.68523.4897
103.8914-0.01560.54883.7192-0.39193.6611-0.07930.18280.1114-0.12250.0035-0.11460.03250.15730.07150.1166-0.0041-0.00960.08560.00210.1263-1.972-8.20194.0767
112.2064-0.23260.64754.0190.40192.4116-0.0638-0.0154-0.2203-0.42840.2079-0.33960.38190.07470.02780.26220.01910.05090.19160.00580.27493.855-18.74884.8006
124.3303-0.6247-0.05992.4471-0.04872.8511-0.1412-0.4213-0.15670.06010.06830.14640.1288-0.15220.07390.17450.00720.0010.11560.00820.1384-7.6973-13.122213.0291
132.9609-0.377-0.86112.26580.37193.50630.00150.0704-0.36620.02530.0630.20.1009-0.2457-0.06770.13570.0054-0.00350.15730.03190.2333-21.5086-8.67086.3017
143.7275-0.1711-2.82362.1135-0.75477.31770.41240.19970.2302-0.05680.0270.2463-0.6932-0.0822-0.2960.27510.06490.0170.23370.04340.3139-24.32624.2693-1.7306
154.05730.2649-1.0313.4152-1.00875.78990.1894-0.46990.11860.29650.14940.1322-0.1746-0.3632-0.21010.19110.0337-0.01260.18990.0120.2525-22.5788-1.149310.1165
163.41360.83350.73734.10551.07653.28760.0316-0.12740.2550.20610.1101-0.4036-0.01820.2525-0.13010.1486-0.00470.00260.2091-0.08480.2403-32.34220.084756.4319
172.67030.38412.23652.85550.64894.7232-0.0012-0.44580.46990.1637-0.09930.20790.0326-0.350.04480.16010.00230.05810.2802-0.08160.2781-46.1469-0.0355.3502
183.9863-0.39680.60978.4261-1.83974.190.2423-0.13650.0314-0.1193-0.3760.03710.319-0.06630.0670.1955-0.0335-0.00030.2398-0.03690.1929-48.2008-9.123449.7194
193.8674-0.9209-0.21162.9147-0.08763.4575-0.0567-0.28380.00840.25-0.0438-0.05870.11720.04980.08560.1516-0.0291-0.0250.12270.00450.155220.0563-23.971634.2891
203.1119-0.21360.43914.11581.1455.10880.0278-0.05260.0421-0.0821-0.01860.04660.0473-0.17560.00330.1083-0.0183-0.00070.095-0.00250.11725.9069-24.951527.0443
213.8908-1.0261.35695.04910.16471.8844-0.16580.14540.3461-0.06140.10590.0082-0.2454-0.14160.06120.14830.0009-0.01860.15410.02810.15699.5991-16.08122.0697
223.972-0.15991.16673.8361-0.24975.493-0.06270.073-0.04540.0175-0.0784-0.13710.02870.11980.15410.0682-0.0190.03170.13220.00860.170722.8606-23.389726.5748
232.8560.77930.02091.38050.07793.92980.018-0.15410.06640.08190.0311-0.1390.0155-0.0412-0.03540.19220.0179-0.01150.1718-0.00440.239129.8255-19.674736.0714
244.8612-0.9266-0.0171.51920.86086.52710.10920.31270.4461-0.097-0.0202-0.1058-0.45050.292-0.07520.1594-0.0337-0.03740.1302-0.0030.232427.7976-13.886231.9518
255.7076-2.08660.72765.896-0.2144.01360.01740.24750.30160.13040.0253-0.3394-0.01180.44120.11560.1628-0.00510.00040.19080.07350.238933.0422-3.11926.8551
263.7058-1.67271.0133.2224-0.79722.72210.05450.2207-0.3186-0.16980.02520.24080.20910.1052-0.10580.2015-0.0055-0.00410.14410.03470.241625.5167-10.13293.3045
272.0190.5076-1.13462.52730.48921.5673-0.15790.6770.7512-0.39030.18470.83160.1693-0.29910.06010.3589-0.0948-0.09890.33880.17530.502313.22040.2349-4.6744
285.0257-2.83951.6715.92991.63832.885-0.2380.16690.3640.02210.149-0.0955-0.02380.26490.08920.1787-0.0247-0.01720.20650.10570.268324.85243.26944.7028
295.01110.29790.75725.0039-0.68315.7685-0.10020.7622-0.0667-0.2916-0.1004-0.32580.32290.48580.14630.16460.00920.04790.32090.03870.209637.0842-7.42322.3717
303.4290.60651.56944.0457-1.57016.9283-0.35350.73720.637-0.1950.3223-0.1514-0.33340.7419-0.06080.256-0.02570.02720.28870.06630.340542.11292.66247.5347
315.42262.92111.49846.51421.64412.75650.20460.0054-0.8431-0.1587-0.2283-0.09380.1325-0.11380.05970.28340.07290.03610.30040.03290.405542.1985-17.60799.8127
324.6612-1.64790.34757.8494-1.42984.3447-0.0203-0.11630.21920.1821-0.199-0.1177-0.34990.45890.12770.18470.02020.01570.27490.02450.22839.9379-6.031411.7487
334.2464-0.25961.49551.654-1.14674.46320.013-0.07390.0899-0.01040.05550.2504-0.0722-0.0966-0.06750.1611-0.01550.02130.0763-0.03820.144-0.737918.504522.4072
347.7021-1.144.99253.7316-2.72284.31810.30640.141-0.50410.0104-0.03330.4120.4523-0.0857-0.18020.2299-0.04660.03250.163-0.01020.203-4.27836.891922.9922
352.87980.44080.40422.0841-0.73512.44880.087-0.3639-0.0230.2438-0.04160.0923-0.1185-0.0379-0.04020.199-0.00370.01190.13510.00020.13171.775714.4534.5979
360.5249-0.52740.84753.23770.65523.5920.02810.21730.0565-0.22910.0008-0.1570.0970.59320.07410.18110.00180.03350.261-0.00710.1733.448914.902515.5632
373.83341.40750.90961.5267-0.25823.26340.084-0.1896-0.4888-0.183-0.0419-0.15360.55970.2003-0.0580.23340.11760.01940.2364-0.00370.2509-28.7447-26.057331.6852
382.73720.80381.9370.84550.1352.511-0.11210.0357-0.42030.01290.2588-0.15030.07750.7131-0.02670.20310.13970.02650.4023-0.00530.2548-19.5043-21.109129.4216
392.23091.11930.19050.9136-0.0552.01170.15590.1364-0.552-0.1996-0.106-0.25880.50740.869-0.02410.29330.2224-0.00030.7093-0.03310.3137-12.8436-22.946631.5777
402.9204-1.02982.39643.2134-0.84511.96790.0219-0.4824-0.57780.12870.1137-0.42450.4970.6595-0.26040.38020.1937-0.0510.81190.13860.3954-9.3735-25.583844.3986
414.42870.15252.42780.92280.23431.7658-0.2036-0.47660.21110.1133-0.07-0.1081-0.07550.67990.27330.19010.03340.01190.54080.0140.2457-16.8007-14.159339.7587
426.35011.30221.45584.6820.35924.12840.128-1.05330.00990.4147-0.19750.05370.29450.23-0.00590.23470.05940.010.4585-0.03330.2291-26.0787-19.085242.7892
435.4262-0.4114-0.13225.86780.82445.53260.13740.28420.4163-0.534-0.1605-0.0691-0.05120.2970.09140.17470.06910.01780.3028-0.00630.206-31.6407-17.93730.4828
443.6687-2.02680.0834.3203-1.09414.5746-0.0094-0.4371-0.53380.1395-0.0680.24340.517-0.17930.05980.2299-0.02830.01880.26480.00830.3295-34.7908-26.251937.2694
453.8083-0.7788-1.03361.77910.66494.18950.00920.4599-0.1634-0.33250.0676-0.03960.1740.09160.11740.21580.0013-0.00190.2447-0.01540.2288-36.2969-20.589122.6297
464.7549-2.2909-2.10546.13553.35938.35030.1372-0.16520.2969-0.08860.04570.0764-0.424-0.0162-0.13340.21580.0210.01520.1951-0.01150.2084-35.054-15.13928.4432
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 12 )A3 - 12
2X-RAY DIFFRACTION2chain 'A' and (resid 13 through 52 )A13 - 52
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 79 )A53 - 79
4X-RAY DIFFRACTION4chain 'A' and (resid 80 through 111 )A80 - 111
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 140 )A112 - 140
6X-RAY DIFFRACTION6chain 'A' and (resid 141 through 152 )A141 - 152
7X-RAY DIFFRACTION7chain 'A' and (resid 153 through 161 )A153 - 161
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 27 )B3 - 27
9X-RAY DIFFRACTION9chain 'B' and (resid 28 through 38 )B28 - 38
10X-RAY DIFFRACTION10chain 'B' and (resid 39 through 68 )B39 - 68
11X-RAY DIFFRACTION11chain 'B' and (resid 69 through 79 )B69 - 79
12X-RAY DIFFRACTION12chain 'B' and (resid 80 through 111 )B80 - 111
13X-RAY DIFFRACTION13chain 'B' and (resid 112 through 139 )B112 - 139
14X-RAY DIFFRACTION14chain 'B' and (resid 140 through 152 )B140 - 152
15X-RAY DIFFRACTION15chain 'B' and (resid 153 through 162 )B153 - 162
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 111 )C3 - 111
17X-RAY DIFFRACTION17chain 'C' and (resid 112 through 139 )C112 - 139
18X-RAY DIFFRACTION18chain 'C' and (resid 140 through 161 )C140 - 161
19X-RAY DIFFRACTION19chain 'D' and (resid 4 through 38 )D4 - 38
20X-RAY DIFFRACTION20chain 'D' and (resid 39 through 79 )D39 - 79
21X-RAY DIFFRACTION21chain 'D' and (resid 80 through 101 )D80 - 101
22X-RAY DIFFRACTION22chain 'D' and (resid 102 through 130 )D102 - 130
23X-RAY DIFFRACTION23chain 'D' and (resid 131 through 152 )D131 - 152
24X-RAY DIFFRACTION24chain 'D' and (resid 153 through 162 )D153 - 162
25X-RAY DIFFRACTION25chain 'E' and (resid 3 through 12 )E3 - 12
26X-RAY DIFFRACTION26chain 'E' and (resid 13 through 68 )E13 - 68
27X-RAY DIFFRACTION27chain 'E' and (resid 69 through 79 )E69 - 79
28X-RAY DIFFRACTION28chain 'E' and (resid 80 through 111 )E80 - 111
29X-RAY DIFFRACTION29chain 'E' and (resid 112 through 130 )E112 - 130
30X-RAY DIFFRACTION30chain 'E' and (resid 131 through 139 )E131 - 139
31X-RAY DIFFRACTION31chain 'E' and (resid 140 through 152 )E140 - 152
32X-RAY DIFFRACTION32chain 'E' and (resid 153 through 161 )E153 - 161
33X-RAY DIFFRACTION33chain 'F' and (resid 3 through 27 )F3 - 27
34X-RAY DIFFRACTION34chain 'F' and (resid 28 through 38 )F28 - 38
35X-RAY DIFFRACTION35chain 'F' and (resid 39 through 121 )F39 - 121
36X-RAY DIFFRACTION36chain 'F' and (resid 122 through 161 )F122 - 161
37X-RAY DIFFRACTION37chain 'G' and (resid 3 through 27 )G3 - 27
38X-RAY DIFFRACTION38chain 'G' and (resid 28 through 52 )G28 - 52
39X-RAY DIFFRACTION39chain 'G' and (resid 53 through 68 )G53 - 68
40X-RAY DIFFRACTION40chain 'G' and (resid 69 through 79 )G69 - 79
41X-RAY DIFFRACTION41chain 'G' and (resid 80 through 101 )G80 - 101
42X-RAY DIFFRACTION42chain 'G' and (resid 102 through 111 )G102 - 111
43X-RAY DIFFRACTION43chain 'G' and (resid 112 through 121 )G112 - 121
44X-RAY DIFFRACTION44chain 'G' and (resid 122 through 136 )G122 - 136
45X-RAY DIFFRACTION45chain 'G' and (resid 137 through 151 )G137 - 151
46X-RAY DIFFRACTION46chain 'G' and (resid 152 through 162 )G152 - 162

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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