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- PDB-5uaq: Escherichia coli RNA polymerase RpoB H526Y mutant -

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基本情報

登録情報
データベース: PDB / ID: 5uaq
タイトルEscherichia coli RNA polymerase RpoB H526Y mutant
要素
  • (DNA-directed RNA polymerase subunit ...) x 4
  • RNA polymerase sigma factor RpoD
キーワードTRANSFERASE / inhibitor / antibiotic / tuberculosis / rifampin / rifamycin / RNA polymerase / RpoB H526Y
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 / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / ribonucleoside binding / : / : / : / : / : / : / DNA-directed RNA polymerase / response to heat / protein-containing complex assembly / intracellular iron ion homeostasis / protein dimerization activity / response to antibiotic / negative regulation of DNA-templated transcription / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
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 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / Topoisomerase I; Chain A, domain 4 / DNA-directed RNA polymerase, insert domain / : / 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 Alpha Subunit; Chain A, domain 2 / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / 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 / Gyrase A; domain 2 / 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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / 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, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 superfamily / RPB6/omega subunit-like superfamily / 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 Rpb1, clamp domain superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / DNA-directed RNA polymerase, insert domain superfamily / 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, RBP11-like subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / 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 / 解像度: 3.6 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 1.42024年3月6日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
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)920,17418
ポリマ－919,86412
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)460,0879
ポリマ－459,9326
非ポリマー1553
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area38130 Å2
ΔGint-185 kcal/mol
Surface area159530 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)460,0879
ポリマ－459,9326
非ポリマー1553
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area36590 Å2
ΔGint-174 kcal/mol
Surface area153750 Å2
手法PISA
単位格子
Length a, b, c (Å)185.361, 206.280, 308.685
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: 150845.906 Da / 分子数: 2 / Mutation: H526Y / 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 / マグネシウムジカチオン


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: 3.21 Å3/Da / 溶媒含有率: 61.66 %
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: 3.6→30 Å / Num. obs: 134049 / % possible obs: 97.3 % / 冗長度: 6.2 % / Net I/σ(I): 12
反射 シェル解像度: 3.6→3.66 Å / CC1/2: 0.665

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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
精密化解像度: 3.6→29.901 Å / SU ML: 0.66 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 38.44 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.3049 1932 1.51 %
Rwork0.2462 --
obs0.2471 128333 93.72 %
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
精密化ステップサイクル: LAST / 解像度: 3.6→29.901 Å
タンパク質核酸リガンド溶媒全体
原子数55693 0 6 0 55699
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.02256507
X-RAY DIFFRACTIONf_angle_d2.15276257
X-RAY DIFFRACTIONf_dihedral_angle_d16.94334981
X-RAY DIFFRACTIONf_chiral_restr0.1078682
X-RAY DIFFRACTIONf_plane_restr0.0169999
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.68990.4011210.36267884X-RAY DIFFRACTION83
3.6899-3.78950.45431300.36498543X-RAY DIFFRACTION90
3.7895-3.90070.44261300.3638615X-RAY DIFFRACTION90
3.9007-4.02630.49921260.36938687X-RAY DIFFRACTION91
4.0263-4.16990.41591330.33848690X-RAY DIFFRACTION92
4.1699-4.33640.45561400.31898877X-RAY DIFFRACTION92
4.3364-4.53310.3811340.29358890X-RAY DIFFRACTION93
4.5331-4.77120.31851380.26429071X-RAY DIFFRACTION94
4.7712-5.06880.30551410.2529123X-RAY DIFFRACTION95
5.0688-5.45790.30441450.24449350X-RAY DIFFRACTION97
5.4579-6.00320.32031450.259430X-RAY DIFFRACTION98
6.0032-6.86270.29621480.24649600X-RAY DIFFRACTION99
6.8627-8.61190.23781480.21329678X-RAY DIFFRACTION99
8.6119-29.90210.23541530.18349963X-RAY DIFFRACTION99
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)
11.3084-0.86820.07361.7749-1.10860.9931-0.01990.50230.0684-0.80610.11570.2232-0.34460.1225-0.00011.4144-0.17250.05231.5822-0.08381.0737-97.936429.1365-39.5322
21.0829-0.90050.41662.03490.25670.9467-0.03830.4060.2301-0.716-0.0232-0.0621-0.0761-0.0865-01.7878-0.17110.11891.70150.07831.2569-94.237427.2836-38.6905
3-0.38750.0918-0.6410.16240.7849-0.244-0.6635-0.1912-0.7121-1.02150.21250.9752-0.02520.6812-0.00012.3553-0.1719-0.02822.52820.32042.1069-65.746359.9465-23.2648
42.09750.8514-0.43721.8644-0.61290.1568-0.2640.93620.35051.68570.27911.40850.47890.86490.07151.46630.48030.01921.8529-0.25870.9538-73.872211.633-30.0785
51.456-0.0149-0.17930.5787-0.31410.00350.87240.09940.1931-1.062-0.12160.46480.9211.17370.00332.68920.69350.02312.3432-0.60431.9859-65.2139-23.2834-36.5276
62.902-0.10870.4520.59070.07910.99340.05830.23350.1161-0.3838-0.3715-1.17680.72910.7421-0.06191.86980.39920.35882.0685-0.24151.3435-74.96823.2305-34.2399
70.8021-0.6538-0.08061.54180.84371.1383-0.0122-0.1490.0219-0.3571-0.23280.3704-0.5813-0.61040.00020.97270.1038-0.11251.2993-0.1941.0609-130.141943.00589.0095
8-0.5201-0.23650.21372.3526-0.1142.04040.09220.1681-0.21071.31460.04130.52770.33990.3862-0.00012.04840.1790.47951.7884-0.04491.545-141.36778.413349.5814
91.2156-0.2962-0.68231.7187-1.5031.5139-0.0171-0.2255-0.25510.5536-0.04270.1586-0.5927-0.05880.00011.3373-0.03740.10982.0286-0.08951.4573-135.022928.339936.5879
100.1741-0.32330.37891.29170.15171.0623-0.0089-0.01560.07220.0154-0.0460.04830.2579-0.16020.00010.6643-0.047-0.05331.1169-0.08330.9869-126.600526.49622.0402
110.97010.20830.34370.3799-0.28830.468-0.09210.28040.2042-0.18070.20830.12630.060.0765-00.9198-0.0149-0.01631.2096-0.05861.1169-111.051138.1378-17.3422
120.1602-0.1933-0.2724-0.629-0.46621.59720.20320.19310.01280.0354-0.0774-0.1-0.03860.056800.85530.01090.0051.1262-0.13651.1066-83.306525.82077.7089
130.5717-0.5134-0.43361.93130.75351.4453-0.07990.0561-0.05550.3249-0.07930.1888-0.22670.0634-0.00010.7007-0.04030.10310.9508-0.03021.0431-87.574238.893244.1843
140.5373-0.06160.150.0907-0.21820.8220.16590.0682-0.2584-0.0227-0.1321-0.03270.37690.069901.1167-0.0150.02850.9439-0.16611.1105-88.5724-1.110911.1115
150.3339-0.34720.09340.2167-0.01530.29120.84021.4186-1.89830.18210.2762-1.52240.15880.79320.00181.68310.1110.14332.2221-0.16862.664-59.37313.46553.3855
160.116-0.0051-0.08660.06880.04880.21430.1113-0.7286-1.15830.94270.25481.1227-2.22820.67020.01822.3437-0.1770.01842.2168-0.31772.7314-40.929124.776417.217
170.3969-0.10450.44790.4596-0.69360.69850.77-0.44590.1778-0.4705-1.0655-0.0252-0.2848-1.19280.00111.3784-0.07620.41331.4848-0.30311.5752-108.766758.825564.106
181.631-0.8638-0.23641.00110.47190.21-0.23550.62510.0599-0.201-0.3307-0.0170.9327-0.2982-0.00082.905-0.21110.55371.7794-0.04692.1278-88.380986.179668.0888
19-0.11690.30040.04620.6107-0.31610.07260.3333-0.2434-0.40970.3039-0.4029-1.809-1.76910.55490.00023.0516-0.1899-0.69162.1960.18493.0889-74.585560.303583.9583
20-0.4238-0.2697-1.25171.5877-0.84161.31780.12960.18480.18790.3158-0.05930.4351-0.6413-0.1195-0.00011.2385-0.03630.19531.1986-0.14691.4513-101.948963.623846.4886
210.7042-0.73430.48960.49910.09581.55940.60030.6024-1.47320.2402-0.4082-0.4643-0.33130.1752-0.00041.1553-0.01980.0811.3407-0.25341.3778-70.687648.44848.5627
220.64670.44740.04380.3573-0.45780.643-0.2537-1.0310.82890.1916-0.291.4106-0.19830.1591-0.00011.5823-0.11540.19061.8903-0.07242.0444-55.58164.25331.2375
23-0.18630.4634-0.26430.268-1.64740.15610.09950.2373-0.4393-0.2772-0.0881-0.5311-0.39060.886-0.0051.8295-0.22460.96882.3291-0.52873.221917.6079-41.917733.4165
240.381-0.18380.88321.5679-1.20812.89481.03570.09761.2215-2.80770.4975-1.36460.7363-0.62510.33621.99070.10450.94112.1829-0.45222.69386.1135-51.960830.304
250.86710.55170.15335.8646-4.17673.2555-0.1326-0.4249-1.00771.7748-1.7836-1.4221-0.5062-0.2695-1.30181.9905-0.42941.48881.9812-0.80092.958717.9971-21.909222.1932
260.20240.1657-0.18970.25530.1380.4860.56930.03410.470.03230.12971.64590.14480.87780.00072.3361-0.28410.45032.2106-1.00262.9094-4.4986-24.714210.8411
270.3139-0.08930.48160.31490.051.0163-1.2621-0.5615-1.4486-0.1673-0.34040.95-0.29790.9257-0.07451.4929-0.38690.5372.08510.06692.0723.4883-16.109218.6265
280.3005-0.03540.17110.076-0.18240.1137-1.3175-0.4303-1.21360.4828-1.0124-1.6413-0.7871.67590.0073.2763-0.82070.16722.370.40982.4673.906214.169611.2404
290.44660.38130.82510.20090.41240.6765-0.2481.05090.8211-0.2294-0.09740.15590.00491.0050.00032.9691-0.43710.68672.61640.35932.4845-3.52312.47013.1801
300.05250.06750.08860.1010.19250.180.18010.1990.3695-0.08771.1389-0.4236-0.7548-1.2236-0.0023.8687-1.23050.77743.09190.05612.5755-4.469422.61413.0402
31-0.029-0.0126-0.13760.06840.06070.0127-0.9032-1.4986-1.09790.5502-0.34590.4010.3219-2.28880.00182.4362-0.53640.44933.11130.16622.33697.0284.971613.0705
320.63790.23561.09540.05780.28511.61471.17840.10760.665-0.1557-0.204-0.24220.2111.06150.61632.2177-0.55760.93672.1108-0.27712.5378-6.5701-25.423218.7346
330.25890.22860.27940.15050.26450.3273-0.48010.39750.86530.4280.50480.23780.7078-0.16890.00012.6214-0.46071.10271.9933-0.33562.5059-4.9218-14.663611.1153
340.0552-0.01840.0386-0.1361-0.06030.03110.0260.118-0.06770.0819-0.0282-0.43391.86630.97430.01142.4956-0.13491.09372.40320.26182.44099.7567-18.28238.0335
351.85841.0031-0.47631.2049-0.70750.3817-0.0999-0.4123-0.6080.479-0.2268-1.09860.14940.0972-0.00022.1288-0.05930.14631.8282-0.15061.7209-13.1839-56.595181.2642
363.03-0.3039-0.76152.59870.43082.6686-0.38940.23190.1239-0.36070.35170.21440.2439-0.42350.00011.7595-0.0579-0.02451.61450.11591.3373-47.4068-27.999103.9381
370.88-0.8082-1.040.24690.47360.3774-0.2446-0.81450.0757-0.61580.3506-0.8375-0.14230.4091-0.00012.0319-0.14650.04291.5946-0.00511.6187-29.1068-43.380691.1935
380.24930.3753-0.63633.1884-1.4168-0.4332-0.08420.03150.03270.5440.1118-0.02390.0550.12150.00041.787-0.08460.10161.5977-0.27861.701-12.0048-33.432476.7953
39-0.3347-0.2494-0.15331.0176-0.6591.3395-0.14290.2578-0.022-0.37930.2516-1.02120.1180.4366-0.00011.2551-0.0250.22941.6866-0.47212.2781.0144-48.267554.0613
401.0351-0.8018-0.02272.51160.36641.0106-0.2421-0.3247-0.2684-0.38130.2702-0.8685-0.1765-0.3631-0.00091.8854-0.09230.34121.693-0.30111.9948-9.7561-69.716944.0521
41-0.8604-0.1043-0.97280.8913-1.7737-0.0740.10450.02340.37340.55380.0361-0.8236-0.3270.7335-0.00631.78020.0653-0.00351.9773-0.85732.27986.8315-62.465962.4734
421.1637-0.76790.3674-0.2899-0.21670.0387-0.1853-0.11990.0063-0.05450.3099-0.2849-0.23220.11120.00011.4122-0.17910.34691.5778-0.31581.70893.7967-27.350550.5312
430.5943-0.3265-1.11140.7924-0.2570.2213-0.04720.53050.2624-0.99810.43880.0918-0.2226-0.2011-0.00021.6756-0.07820.25531.2704-0.06771.1752-47.0407-42.27734.7359
442.015-0.3901-1.33851.9470.15172.6108-0.14750.2525-0.2434-0.00930.0550.2485-0.1157-0.15210.00011.1883-0.06640.17890.98760.00891.0405-66.3136-54.394557.4018
452.23210.861-0.56840.70130.14830.665-0.0680.10690.0278-0.25950.2882-0.06170.23920.1472-0.00031.45790.00070.40341.2207-0.07411.3101-32.6249-44.504338.1583
460.23931.01230.39211.76970.27890.2255-0.12810.24540.0931-0.34330.2568-0.2004-0.08160.0752-01.6335-0.19920.62551.2774-0.07761.4461-18.951-12.637330.321
470.33830.30981.74020.2664-0.5356-0.6123-0.1083-0.27870.33880.22770.20820.0964-0.5952-0.5068-0.00022.0538-0.03040.53491.6682-0.36621.7042-23.0278-4.527358.1632
481.1861-0.858-1.01282.21170.75443.1274-0.21510.03290.6754-0.14040.0191-0.3035-0.1976-0.29080.00021.42020.05040.29591.0825-0.0651.4899-54.6887-5.961952.4617
49-0.08390.3041-0.16890.89280.1325-0.24450.18180.5410.47990.1622-0.1140.6826-0.1929-0.041401.62370.05410.07381.15090.17781.3545-57.6732-30.243742.879
500.0537-0.0023-0.02070.01260.01640.01340.09740.135-0.0465-0.50970.57430.3348-0.0524-0.26890.00023.3202-0.080.60681.90530.1552.3898-30.4972-21.750419.0714
510.0368-0.11130.10230.0429-0.11850.154-1.41361.72370.946-1.14650.4837-0.94451.2139-0.0336-0.00153.49210.79340.41513.2547-0.26913.0212-42.6933-24.893417.8771
52-0.0136-0.01060.0324-0.0021-0.04810.08470.31521.1828-0.0567-0.75991.57761.31411.0936-1.5408-0.00154.2546-0.06030.55823.69910.57912.3374-34.4699-32.4537.9831
530.0140.0089-0.01460.0026-0.0116-0.0219-0.43850.2678-0.2354-0.70810.02680.6105-0.35950.40380.00064.1964-1.3659-0.27954.19240.81472.8228-38.1818-24.661911.8562
54-0.0065-0.08670.02810.0803-0.0480.03391.4697-0.4985-0.6134-0.4170.75050.39360.6827-0.1459-0.00064.281-0.4331-0.81872.8315-0.39953.3988-54.8395-32.8173.8875
550.4958-0.270.29550.1945-0.24640.10120.6458-0.74280.33072.0949-0.74780.70820.0760.1090.00072.36210.1020.45051.66640.07561.6602-72.2331-73.109783.9145
561.79761.37640.88311.6175-0.21190.87120.07950.47150.7055-0.2309-0.0026-0.5323-0.3060.10580.00022.86120.01080.33061.7192-0.01372.2934-87.6275-95.331266.8148
570.2074-0.0171-0.1017-0.024-0.0230.0181.06661.0489-1.63040.4686-0.81760.96820.509-1.2604-0.00133.2766-0.3303-0.99832.98540.03444.2283-113.7392-71.504760.7016
580.52930.48640.16111.540.65550.7728-0.13360.3223-0.55390.2355-0.09620.15840.4633-0.0652-0.00022.0043-0.02570.21851.2360.0051.5911-73.6171-78.281173.6377
591.03010.1343-0.56370.54780.77521.3241-0.3195-0.4892-0.08-0.93320.4062-0.37490.24370.7839-0.00041.8310.3040.30581.46230.00231.6334-33.5574-77.368264.3469
601.77040.4482-0.5548-0.0466-0.03930.39420.37270.0340.7394-0.426-0.75840.4892-1.5808-1.12640.00152.14160.11130.18991.361-0.10951.4125-39.2122-61.130125.7164
610.8035-1.0465-0.24791.36460.0870.5204-0.67410.295-1.2235-1.68550.9403-0.16351.0169-0.09870.00112.8179-0.09960.18921.8118-0.12631.7636-41.0169-76.21579.2014
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 119 )
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 232 )
3X-RAY DIFFRACTION3chain 'A' and (resid 233 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid 6 through 49 )
5X-RAY DIFFRACTION5chain 'B' and (resid 50 through 150 )
6X-RAY DIFFRACTION6chain 'B' and (resid 151 through 233 )
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 158 )
8X-RAY DIFFRACTION8chain 'C' and (resid 159 through 358 )
9X-RAY DIFFRACTION9chain 'C' and (resid 359 through 437 )
10X-RAY DIFFRACTION10chain 'C' and (resid 438 through 767 )
11X-RAY DIFFRACTION11chain 'C' and (resid 768 through 1210 )
12X-RAY DIFFRACTION12chain 'C' and (resid 1211 through 1342 )
13X-RAY DIFFRACTION13chain 'D' and (resid 8 through 354 )
14X-RAY DIFFRACTION14chain 'D' and (resid 355 through 1376 )
15X-RAY DIFFRACTION15chain 'E' and (resid 2 through 60 )
16X-RAY DIFFRACTION16chain 'E' and (resid 61 through 90 )
17X-RAY DIFFRACTION17chain 'F' and (resid 95 through 135 )
18X-RAY DIFFRACTION18chain 'F' and (resid 136 through 262 )
19X-RAY DIFFRACTION19chain 'F' and (resid 263 through 333 )
20X-RAY DIFFRACTION20chain 'F' and (resid 334 through 510 )
21X-RAY DIFFRACTION21chain 'F' and (resid 511 through 562 )
22X-RAY DIFFRACTION22chain 'F' and (resid 563 through 612 )
23X-RAY DIFFRACTION23chain 'G' and (resid 8 through 138 )
24X-RAY DIFFRACTION24chain 'G' and (resid 139 through 179 )
25X-RAY DIFFRACTION25chain 'G' and (resid 180 through 231 )
26X-RAY DIFFRACTION26chain 'H' and (resid 6 through 34 )
27X-RAY DIFFRACTION27chain 'H' and (resid 35 through 49 )
28X-RAY DIFFRACTION28chain 'H' and (resid 50 through 69 )
29X-RAY DIFFRACTION29chain 'H' and (resid 70 through 133 )
30X-RAY DIFFRACTION30chain 'H' and (resid 134 through 145 )
31X-RAY DIFFRACTION31chain 'H' and (resid 146 through 179 )
32X-RAY DIFFRACTION32chain 'H' and (resid 180 through 197 )
33X-RAY DIFFRACTION33chain 'H' and (resid 198 through 212 )
34X-RAY DIFFRACTION34chain 'H' and (resid 213 through 234 )
35X-RAY DIFFRACTION35chain 'I' and (resid 3 through 158 )
36X-RAY DIFFRACTION36chain 'I' and (resid 159 through 408 )
37X-RAY DIFFRACTION37chain 'I' and (resid 409 through 481 )
38X-RAY DIFFRACTION38chain 'I' and (resid 482 through 688 )
39X-RAY DIFFRACTION39chain 'I' and (resid 689 through 863 )
40X-RAY DIFFRACTION40chain 'I' and (resid 864 through 979 )
41X-RAY DIFFRACTION41chain 'I' and (resid 980 through 1084 )
42X-RAY DIFFRACTION42chain 'I' and (resid 1085 through 1271 )
43X-RAY DIFFRACTION43chain 'I' and (resid 1272 through 1342 )
44X-RAY DIFFRACTION44chain 'J' and (resid 16 through 307 )
45X-RAY DIFFRACTION45chain 'J' and (resid 308 through 405 )
46X-RAY DIFFRACTION46chain 'J' and (resid 406 through 649 )
47X-RAY DIFFRACTION47chain 'J' and (resid 650 through 854 )
48X-RAY DIFFRACTION48chain 'J' and (resid 855 through 1301 )
49X-RAY DIFFRACTION49chain 'J' and (resid 1302 through 1375 )
50X-RAY DIFFRACTION50chain 'K' and (resid 2 through 6 )
51X-RAY DIFFRACTION51chain 'K' and (resid 7 through 31 )
52X-RAY DIFFRACTION52chain 'K' and (resid 32 through 45 )
53X-RAY DIFFRACTION53chain 'K' and (resid 46 through 60 )
54X-RAY DIFFRACTION54chain 'K' and (resid 61 through 80 )
55X-RAY DIFFRACTION55chain 'L' and (resid 94 through 135 )
56X-RAY DIFFRACTION56chain 'L' and (resid 136 through 292 )
57X-RAY DIFFRACTION57chain 'L' and (resid 293 through 333 )
58X-RAY DIFFRACTION58chain 'L' and (resid 334 through 446 )
59X-RAY DIFFRACTION59chain 'L' and (resid 447 through 510 )
60X-RAY DIFFRACTION60chain 'L' and (resid 511 through 562 )
61X-RAY DIFFRACTION61chain 'L' and (resid 563 through 613 )

+
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