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- PDB-5uaj: Escherichia coli RNA polymerase RpoB S531L mutant -

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基本情報

登録情報
データベース: PDB / ID: 5uaj
タイトルEscherichia coli RNA polymerase RpoB S531L mutant
要素
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
キーワードtransferase/transferase inhibitor / inhibitor / antibiotic / tuberculosis / rifampin / rifamycin / RNA polymerase / RpoB S531L / transferase-transferase inhibitor complex
機能・相同性
機能・相同性情報


sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type RNA polymerase core enzyme binding / cytosolic DNA-directed RNA polymerase complex / bacterial-type flagellum-dependent cell motility / nitrate assimilation / regulation of DNA-templated transcription elongation / transcription elongation factor complex / transcription antitermination / DNA-directed RNA polymerase complex / cell motility / DNA-templated transcription initiation / ribonucleoside binding / DNA-directed RNA polymerase / DNA-directed RNA polymerase activity / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / transcription cis-regulatory region binding / response to antibiotic / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytoplasm / cytosol
類似検索 - 分子機能
RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit ...RNA Polymerase Primary Sigma Factor / RNA Polymerase Primary Sigma Factor / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / RNA polymerase II, Rpb2 subunit, wall domain / RNA polymerase subunit, RPB6/omega / Eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb1 funnel domain / RNA polymerase, RBP11-like subunit / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / Sigma-70 factors family signature 1. / RNA Polymerase Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / : / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / Gyrase A; domain 2 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, omega subunit / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / DNA-directed RNA polymerase, beta subunit, external 1 domain superfamily / DNA-directed RNA polymerase, beta subunit, external 1 domain / RNA polymerase beta subunit external 1 domain / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase beta subunit, bacterial-type / DNA-directed RNA polymerase, alpha subunit / Beta Complex / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / RNA polymerase Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, OB-fold / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 3 / RNA polymerases beta chain signature. / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 6 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Alpha-Beta Complex / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
類似検索 - ドメイン・相同性
RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
類似検索 - 構成要素
生物種Escherichia coli (大腸菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 3.915 Å
データ登録者Molodtsov, V. / Scharf, N.T. / Stefan, M.A. / Garcia, G.A. / Murakami, K.S.
資金援助 米国, 2件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM087350 米国
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI110780 米国
引用ジャーナル: Mol. Microbiol. / 年: 2017
タイトル: Structural basis for rifamycin resistance of bacterial RNA polymerase by the three most clinically important RpoB mutations found in Mycobacterium tuberculosis.
著者: Molodtsov, V. / Scharf, N.T. / Stefan, M.A. / Garcia, G.A. / Murakami, K.S.
履歴
登録2016年12月19日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02017年1月11日Provider: repository / タイプ: Initial release
改定 1.12017年3月22日Group: Database references
改定 1.22017年9月20日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.32019年12月11日Group: Author supporting evidence / カテゴリ: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
改定 1.42023年10月4日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)920,17618
ポリマ－919,86612
非ポリマー3106
水00
1
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)460,0889
ポリマ－459,9336
非ポリマー1553
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area37610 Å2
ΔGint-191 kcal/mol
Surface area155030 Å2
手法PISA
2
G: DNA-directed RNA polymerase subunit alpha
H: DNA-directed RNA polymerase subunit alpha
I: DNA-directed RNA polymerase subunit beta
J: DNA-directed RNA polymerase subunit beta'
K: DNA-directed RNA polymerase subunit omega
L: RNA polymerase sigma factor RpoD
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)460,0889
ポリマ－459,9336
非ポリマー1553
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36970 Å2
ΔGint-185 kcal/mol
Surface area154000 Å2
手法PISA
単位格子
Length a, b, c (Å)187.219, 204.426, 310.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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要素

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DNA-directed RNA polymerase subunit ... , 4種, 10分子 ABGHCIDJEK

#1: タンパク質
DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / RNA polymerase subunit alpha / Transcriptase subunit alpha


分子量: 36558.680 Da / 分子数: 4 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoA, pez, phs, sez, b3295, JW3257 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A7Z4, DNA-directed RNA polymerase
#2: タンパク質 DNA-directed RNA polymerase subunit beta / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


分子量: 150846.953 Da / 分子数: 2 / Mutation: S531L / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12
遺伝子: rpoB, groN, nitB, rif, ron, stl, stv, tabD, b3987, JW3950
発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A8V2, DNA-directed RNA polymerase
#3: タンパク質 DNA-directed RNA polymerase subunit beta' / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


分子量: 155366.781 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoC, tabB, b3988, JW3951 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A8T7, DNA-directed RNA polymerase
#4: タンパク質 DNA-directed RNA polymerase subunit omega / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


分子量: 10249.547 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoZ, b3649, JW3624 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P0A800, DNA-directed RNA polymerase

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タンパク質 , 1種, 2分子 FL

#5: タンパク質 RNA polymerase sigma factor RpoD / Sigma-70


分子量: 70352.242 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Escherichia coli (strain K12) (大腸菌)
株: K12 / 遺伝子: rpoD, alt, b3067, JW3039 / 発現宿主: Escherichia coli (大腸菌) / 参照: UniProt: P00579

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非ポリマー , 2種, 6分子

#6: 化合物 ChemComp-MG / MAGNESIUM ION


分子量: 24.305 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Mg
#7: 化合物
ChemComp-ZN / ZINC ION


分子量: 65.409 Da / 分子数: 4 / 由来タイプ: 合成 / 式: Zn

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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: 3.23 Å3/Da / 溶媒含有率: 61.93 %
結晶化温度: 300 K / 手法: 蒸気拡散法, ハンギングドロップ法
詳細: 0.1 M HEPES-HCl (pH 6.7), 0.2 M Ca Acetate, 30% PEG400, 10 mM DTT

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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: CHESS / ビームライン: A1 / 波長: 0.9769 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2013年3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: 0.9769 Å / 相対比: 1
反射解像度: 3.9→30 Å / Num. obs: 86257 / % possible obs: 81.3 % / 冗長度: 5.6 % / Net I/σ(I): 11.6
反射 シェル解像度: 3.9→3.97 Å / CC1/2: 0.634

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解析

ソフトウェア
名称バージョン分類
PHENIX(1.10.1_2155: ???)精密化
HKL-2000データ削減
HKL-2000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
開始モデル: 4YG2

4yg2


解像度: 3.915→29.959 Å / SU ML: 0.67 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 37.18
Rfactor反射数%反射
Rfree0.3073 1978 2.33 %
Rwork0.2596 --
obs0.2607 84997 79.09 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å
精密化ステップサイクル: LAST / 解像度: 3.915→29.959 Å
タンパク質核酸リガンド溶媒全体
原子数54988 0 6 0 54994
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00455791
X-RAY DIFFRACTIONf_angle_d0.9575296
X-RAY DIFFRACTIONf_dihedral_angle_d16.52434521
X-RAY DIFFRACTIONf_chiral_restr0.0518577
X-RAY DIFFRACTIONf_plane_restr0.0059875
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9149-4.01260.4261080.3944473X-RAY DIFFRACTION60
4.0126-4.12080.45471400.38285993X-RAY DIFFRACTION81
4.1208-4.24180.44871470.36796117X-RAY DIFFRACTION82
4.2418-4.37830.38661450.36896069X-RAY DIFFRACTION82
4.3783-4.53420.37421450.34556071X-RAY DIFFRACTION82
4.5342-4.71510.41121460.32576071X-RAY DIFFRACTION82
4.7151-4.92880.30641440.30196080X-RAY DIFFRACTION82
4.9288-5.18740.35581440.30616079X-RAY DIFFRACTION81
5.1874-5.51060.32731460.29486093X-RAY DIFFRACTION81
5.5106-5.9330.38951450.28836093X-RAY DIFFRACTION81
5.933-6.52450.39411450.28076066X-RAY DIFFRACTION81
6.5245-7.45580.28231420.2566005X-RAY DIFFRACTION80
7.4558-9.3460.22881400.20255922X-RAY DIFFRACTION78
9.346-29.95990.23451410.1795887X-RAY DIFFRACTION75
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)
11.4279-0.9088-1.05121.3711.8432.41660.07060.5593-0.1764-0.84570.01880.1413-0.2921-0.07190.00011.9199-0.07130.05462.16150.05451.6939-100.635432.9795-39.0522
21.1384-1.05750.3620.8919-0.00920.0717-0.52820.08710.27790.59980.8296-0.4394-0.24260.19550.00042.079-0.1234-0.03912.10020.00621.7163-93.481135.2088-29.0842
30.6942-0.15730.25840.6583-0.88370.73680.05080.94260.3879-0.6926-0.1416-0.06980.8264-0.2592-0.00062.39530.12640.29332.5174-0.01231.8008-87.755712.2064-45.7428
41.01320.33590.07560.49740.33930.2114-0.07830.76020.51130.2114-0.219-0.28171.23310.9988-0.00021.89450.44920.06442.5087-0.01671.8573-74.563612.5239-30.0161
50.1911-0.050.15610.31180.09530.01150.28320.0716-0.0727-1.3214-1.3431-0.7672.2954-1.244-0.00054.6047-0.31470.79822.5615-0.43542.2502-73.351-22.0733-40.1606
63.0736-0.45211.35770.144-0.23860.6308-0.357-0.3093-2.39960.2450.5032-0.16671.5731-0.04080.05983.5530.81610.70262.993-0.52271.9184-70.3785-27.9685-30.1125
70.4840.35970.06360.22990.11410.1458-0.4160.868-0.8021-1.45290.1332-1.22050.97180.9920.00073.3041.08640.34013.2358-0.42452.8547-62.2326-17.9231-42.7588
81.76010.95290.82570.52690.47880.4175-0.13610.81482.40980.5759-0.22231.2083-0.7551.2613-0.14742.74190.16980.85032.8441-0.80323.3443-57.1411-18.7957-36.9772
90.18610.052-0.02310.07330.03570.0249-0.24460.44871.1164-0.90130.43120.31020.21850.8960.00033.14020.49290.26612.2316-0.02882.1996-60.7675-27.4763-27.9482
101.2630.4682-0.42010.3298-0.28910.2763-2.0416-0.41-2.21040.46160.0426-0.1427-0.15940.1126-0.03014.01380.07950.62172.2172-0.36382.0183-63.8249-28.5669-39.8928
110.64960.5466-0.46870.335-0.19070.3017-0.3812-0.1447-0.9361-0.16010.5504-0.97960.00560.2651-0.00082.82830.36440.43022.5521-0.21071.8865-76.8747-6.3994-35.5576
121.29080.9528-0.15290.4781-0.24130.4108-0.05690.3617-0.1310.2045-0.0103-0.63391.09060.683-0.00032.05360.43050.27482.397-0.35011.8585-73.814710.6376-34.2511
130.5916-0.41740.74462.2899-0.13941.8570.2254-0.18030.0205-0.1029-0.31790.1437-1.0619-1.2042-0.00021.64190.1457-0.1192.0592-0.22471.8222-132.923444.44847.7502
14-0.04981.17-1.29620.45050.01630.6990.4648-0.6413-0.00421.5631-0.29670.5223-0.25590.60520.00052.25220.03410.24012.50910.12272.0417-136.323813.567240.0336
150.56190.08860.6608-0.09280.01130.91860.08060.2097-0.90090.38880.24571.6817-0.8134-0.680802.9198-0.35360.39943.75180.33963.502-150.15620.585955.0173
161.3827-0.4031-0.37362.21550.00062.5615-0.2394-0.23060.03560.40130.03950.13610.12-0.666-0.52931.25250.0625-0.09631.8138-0.15821.503-129.059726.45748.0092
171.82580.16090.72830.978-0.09981.3956-0.11850.26640.5809-0.38040.08120.1313-0.2987-0.0568-01.4889-0.0197-0.01141.74610.01591.6026-111.410938.69-16.961
180.4174-0.3117-0.5295-0.0844-0.54681.56590.16020.20930.1887-0.2019-0.2191-0.24-0.07020.182-01.2740.03620.00551.6382-0.08311.5351-83.891626.26368.3391
191.8228-1.0249-0.63474.97770.22682.7381-0.2112-0.1018-0.22990.6994-0.06820.0813-0.03330.4483-0.00011.4265-0.05990.00391.5071-0.09891.664-87.845439.642846.9787
201.5519-0.58230.15550.28230.62462.74980.0415-0.1699-0.0422-0.0219-0.0040.1307-0.01490.672-0.00031.19030.04710.00741.46160.04361.447-86.157829.81710.5586
211.3628-0.07481.06990.90550.37180.93480.13360.0271-0.5771-0.0468-0.0508-0.12470.5950.054601.77690.06820.14051.6281-0.11151.662-90.9284-3.2507-0.2614
221.566-1.2058-0.29682.9134-1.07043.572-0.0353-0.614-0.69240.224-0.16490.16340.80020.06580.00011.5995-0.02010.0611.62390.04331.7804-88.6195-1.107535.7492
230.00790.0452-0.05370.0556-0.0529-0.0031-1.28830.60250.5604-0.03421.1987-1.1448-0.82652.53880.00092.3766-0.0235-0.32722.5794-0.18693.112-65.71645.36624.3107
240.2426-0.037-0.20810.06930.12110.1381.17151.4060.0003-0.01110.9778-0.36360.5474-0.36960.00022.28530.0839-0.0052.42490.09182.8519-58.419616.14162.8705
250.3115-0.2931-0.08840.17920.1327-0.0055-1.1697-0.21560.0085-0.14710.05660.6446-0.85550.45050.00212.8757-0.43450.12062.7239-0.03413.1607-41.552124.305117.2875
260.98440.493-0.13650.26370.06690.29090.107-0.86420.1614-0.5118-0.58310.2895-0.1503-0.58440.00093.4412-0.13520.45842.108-0.19152.414-109.887757.876464.1931
272.6777-0.28271.18750.78820.67080.86350.31940.5104-0.4048-0.4517-0.0566-0.90322.19240.0908-0.00023.20410.1470.24152.2650.01682.8109-86.849379.131769.9367
280.205-0.2949-0.09170.1836-0.0215-0.07781.2626-0.1653-0.8739-0.585-0.7556-0.0089-0.31621.9884-03.4323-0.2716-1.28643.68810.01454.1919-71.300659.653888.8684
291.31060.1963-1.56711.35980.07472.19040.10060.14210.34590.2684-0.06390.2929-0.613-0.0161-02.08030.1267-0.06551.80130.00872.1341-90.660760.210927.911
30-0.0022-0.260.25840.154-0.30730.29460.40951.3272-0.9241-0.5249-0.4891-0.163-0.82871.2853-0.00031.7689-0.18790.36932.5143-0.33493.003618.0263-19.847323.1058
310.93730.34721.00650.52350.15270.8412-0.0450.3575-0.1799-0.49220.0538-0.8082-0.09861.5747-02.390.3070.632.4612-0.26952.981915.5956-52.150737.1507
32-0.16320.1477-0.14590.7593-1.27951.1723-0.1985-0.2206-0.0382-1.38170.0005-0.0670.56120.08970.00012.31540.04140.36762.3865-0.49073.54969.5662-34.189627.586
331.43320.6419-0.43015.353-0.35640.20570.1034-0.9629-0.21911.1396-1.1676-1.57310.56580.0073-0.37931.41710.26991.39912.4487-0.24553.518214.7454-28.329820.1754
342.2654-1.83870.91741.4596-0.07121.7045-0.5830.74810.2713-0.94910.8990.6479-0.520.4387-0.00032.5891-0.10720.39832.20180.13132.5464-1.2453-10.508212.8061
350.0137-0.1095-0.36581.1210.82680.5465-0.1189-0.0210.1768-0.58530.2962-0.3361-0.28510.2430.00012.7584-0.39980.65352.66360.28322.9096-2.451710.61926.3314
360.9128-0.40390.67090.348-0.35140.75010.9077-0.0570.3560.0848-1.1201-0.5215-0.06541.9462-0.00022.1149-0.07270.72132.54030.01162.6979-0.555-20.639811.9453
370.37-0.0557-0.48630.84420.27731.1285-0.1205-0.1712-0.04710.52330.1563-0.16350.36970.1727-0.00042.55560.0927-0.14542.2147-0.02962.1259-23.5169-38.771386.7269
381.9032-0.21740.03880.9365-0.04750.47160.0461-0.1378-0.15070.16690.1534-0.54160.20750.3104-02.04430.0460.17462.1135-0.15852.0469-7.582-46.879848.459
392.9211-0.0678-0.21713.3216-0.36893.9533-0.06290.2589-0.3061-0.0545-0.13260.3992-0.197-0.2318-0.00011.7222-0.08350.09241.53310.07651.606-67.1034-54.185557.9577
400.66250.0089-0.53861.59351.19080.97810.42370.08820.57770.13560.23110.087-0.7525-0.5151-0.0011.84830.23710.21141.77720.1041.7243-36.4608-41.374146.3756
411.08470.51910.3043.05150.10850.63250.03360.11430.3669-0.32960.0859-0.4166-0.22120.1367-0.00012.00090.07740.53921.7623-0.00622.0902-19.6647-13.435536.5434
421.67470.10820.10380.2970.41181.31720.1357-0.32220.62310.0912-0.0278-0.0368-0.534-0.247902.16630.13440.23221.784-0.01932.0651-47.3458-9.929350.8489
430.055800.0343-0.04420.01720.0205-1.52962.05661.3333-1.83361.88630.0957-0.023-1.8116-0.00044.17850.0074-0.13153.38960.32612.9649-39.5909-26.299714.3342
440.026-0.1070.09260.1247-0.12390.1078-0.8896-1.308-0.2112-0.3097-0.2191-0.59290.61870.69660.00054.1999-0.1119-0.40763.5287-0.42623.4536-55.8733-33.07444.0489
450.3841-0.12470.62020.269-0.49620.5353-0.7182-0.8471-0.1220.8438-0.25650.25120.1423-0.2526-02.64460.07690.31422.52590.23182.3279-72.7048-72.628384.5791
461.51821.50811.83262.04850.90391.37430.1081.06550.0999-1.5693-0.30610.2097-0.7224-0.16630.00033.53490.01860.39472.5127-0.14692.7715-88.1024-94.84667.7479
47-0.05730.16730.29950.48810.33730.22951.13970.66980.58-0.5915-1.27561.51080.9427-0.01020.00024.34460.0778-0.62263.14530.05673.6652-110.9303-74.717160.1146
480.8283-0.2301-2.04760.6260.03612.7112-0.2106-0.0189-0.39310.2133-0.0313-0.10610.14450.17420.00012.60240.12620.02431.85980.07342.0657-50.5379-73.068961.7781
491.6224-1.47810.52631.2114-0.56810.9196-0.21280.6979-0.9998-1.1949-0.08350.65990.2976-0.7047-0.00032.52560.18860.3212.4025-0.37332.3638-41.4703-75.90549.5976
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 150 )
2X-RAY DIFFRACTION2chain 'A' and (resid 151 through 186 )
3X-RAY DIFFRACTION3chain 'A' and (resid 187 through 234 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 48 )
5X-RAY DIFFRACTION5chain 'B' and (resid 49 through 68 )
6X-RAY DIFFRACTION6chain 'B' and (resid 69 through 86 )
7X-RAY DIFFRACTION7chain 'B' and (resid 87 through 106 )
8X-RAY DIFFRACTION8chain 'B' and (resid 107 through 126 )
9X-RAY DIFFRACTION9chain 'B' and (resid 127 through 136 )
10X-RAY DIFFRACTION10chain 'B' and (resid 137 through 146 )
11X-RAY DIFFRACTION11chain 'B' and (resid 147 through 190 )
12X-RAY DIFFRACTION12chain 'B' and (resid 191 through 232 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 142 )
14X-RAY DIFFRACTION14chain 'C' and (resid 143 through 254 )
15X-RAY DIFFRACTION15chain 'C' and (resid 255 through 345 )
16X-RAY DIFFRACTION16chain 'C' and (resid 346 through 804 )
17X-RAY DIFFRACTION17chain 'C' and (resid 805 through 1212 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1213 through 1342 )
19X-RAY DIFFRACTION19chain 'D' and (resid 8 through 307 )
20X-RAY DIFFRACTION20chain 'D' and (resid 308 through 393 )
21X-RAY DIFFRACTION21chain 'D' and (resid 394 through 914 )
22X-RAY DIFFRACTION22chain 'D' and (resid 915 through 1376 )
23X-RAY DIFFRACTION23chain 'E' and (resid 2 through 16 )
24X-RAY DIFFRACTION24chain 'E' and (resid 17 through 60 )
25X-RAY DIFFRACTION25chain 'E' and (resid 61 through 90 )
26X-RAY DIFFRACTION26chain 'F' and (resid 94 through 135 )
27X-RAY DIFFRACTION27chain 'F' and (resid 136 through 291 )
28X-RAY DIFFRACTION28chain 'F' and (resid 292 through 354 )
29X-RAY DIFFRACTION29chain 'F' and (resid 355 through 612 )
30X-RAY DIFFRACTION30chain 'G' and (resid 8 through 49 )
31X-RAY DIFFRACTION31chain 'G' and (resid 50 through 150 )
32X-RAY DIFFRACTION32chain 'G' and (resid 151 through 200 )
33X-RAY DIFFRACTION33chain 'G' and (resid 201 through 231 )
34X-RAY DIFFRACTION34chain 'H' and (resid 6 through 69 )
35X-RAY DIFFRACTION35chain 'H' and (resid 70 through 186 )
36X-RAY DIFFRACTION36chain 'H' and (resid 187 through 232 )
37X-RAY DIFFRACTION37chain 'I' and (resid 3 through 787 )
38X-RAY DIFFRACTION38chain 'I' and (resid 788 through 1342 )
39X-RAY DIFFRACTION39chain 'J' and (resid 16 through 307 )
40X-RAY DIFFRACTION40chain 'J' and (resid 308 through 376 )
41X-RAY DIFFRACTION41chain 'J' and (resid 377 through 703 )
42X-RAY DIFFRACTION42chain 'J' and (resid 704 through 1375 )
43X-RAY DIFFRACTION43chain 'K' and (resid 2 through 60 )
44X-RAY DIFFRACTION44chain 'K' and (resid 61 through 80 )
45X-RAY DIFFRACTION45chain 'L' and (resid 94 through 135 )
46X-RAY DIFFRACTION46chain 'L' and (resid 136 through 291 )
47X-RAY DIFFRACTION47chain 'L' and (resid 292 through 354 )
48X-RAY DIFFRACTION48chain 'L' and (resid 355 through 562 )
49X-RAY DIFFRACTION49chain 'L' and (resid 563 through 613 )

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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