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- PDB-5uah: Escherichia coli RNA polymerase and Rifampin complex, RpoB D516V ... -

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基本情報

登録情報
データベース: PDB / ID: 5uah
タイトルEscherichia coli RNA polymerase and Rifampin complex, RpoB D516V 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 D516V mutant / 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 / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation ...sigma factor antagonist complex / RNA polymerase complex / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / bacterial-type flagellum assembly / 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 5'-3' RNA polymerase activity / 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 / cytoplasm / cytosol
類似検索 - 分子機能
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 / Sigma-70 factors family signature 1. / 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 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 / Sigma-70 factors family signature 1. / 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 / 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, alpha subunit / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase Rpb6 / RNA polymerase, subunit omega/Rpo6/RPB6 / RNA polymerase Rpb6 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / RPB6/omega subunit-like superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, beta subunit, protrusion / RNA polymerase beta subunit / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / 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 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 2 / 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 / Winged helix-like DNA-binding domain superfamily
類似検索 - ドメイン・相同性
RIFAMPICIN / 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: 4.1 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 ...Data collection / Database references / Derived calculations / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr2_label_seq_id

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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)920,96421
ポリマ－919,78212
非ポリマー1,1829
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)460,89311
ポリマ－459,8916
非ポリマー1,0025
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
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)460,07010
ポリマ－459,8916
非ポリマー1794
水0
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)187.814, 206.668, 310.286
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: 150804.922 Da / 分子数: 2 / Mutation: D516V / 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 , 3種, 9分子

#6: 化合物 ChemComp-RFP / RIFAMPICIN


分子量: 822.940 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C43H58N4O12 / コメント: 抗生剤*YM
#7: 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: 4 / 由来タイプ: 合成 / 式: Mg
#8: 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: 3.27 Å3/Da / 溶媒含有率: 62.43 %
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: 0.9779 Å
検出器タイプ: ADSC QUANTUM 270 / 検出器: CCD / 日付: 2013年6月11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: 0.9779 Å / 相対比: 1
反射解像度: 4.1→30 Å / Num. obs: 96868 / % possible obs: 99.8 % / 冗長度: 7.4 % / Net I/σ(I): 13.9
反射 シェル最低解像度: 4.17 Å / CC1/2: 0.537

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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: 4.1→29.74 Å / SU ML: 0.61 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 33.73 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2868 1946 2.06 %
Rwork0.2429 --
obs0.2438 94321 99.38 %
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: 4.1→29.74 Å
タンパク質核酸リガンド溶媒全体
原子数55058 0 67 0 55125
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.00855956
X-RAY DIFFRACTIONf_angle_d1.17175492
X-RAY DIFFRACTIONf_dihedral_angle_d16.71434591
X-RAY DIFFRACTIONf_chiral_restr0.068598
X-RAY DIFFRACTIONf_plane_restr0.0069892
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1-4.20230.40231350.35716340X-RAY DIFFRACTION96
4.2023-4.31560.37691370.34476458X-RAY DIFFRACTION99
4.3156-4.44220.35121380.33776543X-RAY DIFFRACTION99
4.4422-4.58510.32641380.31136529X-RAY DIFFRACTION99
4.5851-4.74830.31571350.29586532X-RAY DIFFRACTION100
4.7483-4.93760.31881400.2946586X-RAY DIFFRACTION100
4.9376-5.16120.29421370.29476570X-RAY DIFFRACTION100
5.1612-5.43180.33221390.29196575X-RAY DIFFRACTION100
5.4318-5.76980.37081390.28346609X-RAY DIFFRACTION100
5.7698-6.21150.35561410.29656649X-RAY DIFFRACTION100
6.2115-6.82980.3281390.2776645X-RAY DIFFRACTION100
6.8298-7.80240.29111410.25216689X-RAY DIFFRACTION100
7.8024-9.7720.24791410.19366733X-RAY DIFFRACTION100
9.772-29.7410.22341460.17226917X-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)
12.2761.3924-0.31514.6734-1.80875.08740.0827-0.7634-0.44590.9266-0.4483-0.25590.384-0.09370.34882.36220.03660.03332.46190.0861.853494.494921.344340.8278
28.91523.5298-0.95393.4254-2.20052.82810.2044-1.47060.05990.8409-0.4266-0.1606-0.35510.3370.02392.68720.04670.02672.1159-0.12722.1753106.362642.970138.01
33.63783.9816-1.51112.2484-3.02266.99910.2981-0.50990.3746-0.51390.15891.52220.66640.0693-0.13312.77620.28440.05072.5725-0.16521.873493.07125.062235.4975
43.01731.8824-1.25973.1490.33163.87430.4816-0.81541.0091.1333-0.71660.37170.2166-0.45110.25053.0091-0.03150.36482.5072-0.06471.909284.031319.231841.7048
52.23120.66120.66886.34040.18171.9508-0.7825-0.0524-0.45640.40840.49120.06781.6126-0.50890.24913.2188-0.43950.57172.47640.07582.14474.3003-4.486932.71
63.63980.5569-2.82572.83820.68162.68850.2298-0.7666-0.15820.6081-0.54410.79391.185-0.37830.28173.6002-0.63030.36872.38580.45992.553266.405-19.327439.0721
72.7627-2.1330.8767.55552.35792.17120.3038-0.34540.30370.77470.06741.6361.1989-0.64670.04192.9553-0.48370.27442.56830.221.970375.116210.252632.9576
82.43710.4434-0.89223.4891-0.67092.42850.02370.86180.1264-0.6955-0.1261-0.6804-0.54410.39220.09382.0378-0.1172-0.06052.51780.26292.0738132.732335.2955-18.3915
93.92681.78962.32324.51891.36312.05270.83540.8243-1.3638-2.7020.2127-2.13230.54730.9428-0.65824.11430.24390.53383.5205-0.3243.529152.8953-1.4332-53.608
103.77530.2380.94477.8147-0.09314.51290.03011.2761-0.2297-2.27-0.1451-0.6258-0.3693-0.6856-0.17592.80860.12650.17773.07990.032.1996139.474220.8654-43.5121
112.19791.86340.25814.0136-0.20384.3062-0.00410.46730.0533-0.6150.0636-0.44680.60230.65930.12571.46160.07760.04261.98570.16561.6083128.981823.0135-6.6296
122.1729-0.31990.24051.8360.23821.5159-0.1524-0.19210.5640.51130.1632-0.345-0.180.1137-0.02971.8323-0.0251-0.0262.02740.03741.7028113.155137.369616.8615
133.8152-0.72-4.17767.9051-2.13754.91990.3149-0.19510.4638-0.3895-0.18850.1945-0.002-0.7041-0.21781.62620.01490.01071.45980.00911.505778.35630.0327-18.495
142.5630.3772-1.51376.77410.2876.80310.0710.0918-0.2622-0.6574-0.2142-0.0604-0.155-0.26790.00211.69250.0360.04931.54130.12121.73988.622339.5697-46.4074
151.52130.00350.71440.98620.01091.59050.15270.1668-0.6076-0.1393-0.15070.01470.71620.087-0.02462.2332-0.02770.22381.71280.06241.96289.9807-0.1448-10.7836
162.5274-0.38851.22665.4423-1.4116.2113-0.1494-1.60180.43240.46510.48511.29630.8819-1.5478-0.43342.2008-0.11550.08692.67610.01362.717760.516813.5512-3.1229
172.05541.97191.62217.58960.52831.9409-1.1815-1.0913-0.5868-1.24380.65470.1569-1.6108-0.68110.35173.01070.2292-0.01962.4651-0.14653.018443.618221.6039-14.5557
185.3447-3.3323.07588.77222.31394.6736-0.1736-0.4274-3.0033-1.32541.94140.3213-3.3274-0.5558-1.63623.6210.31530.35873.18090.08662.786634.346538.1066-27.5136
192.4455-3.33232.3349.4324-4.03493.1671-0.2267-0.24580.50630.42050.06150.2092-1.18330.45110.22123.252-0.15440.75822.4011-0.05252.64396.539976.3814-67.3095
201.10860.0807-1.73363.03192.64375.3734-0.30930.7742-0.3067-1.0327-1.32533.1113-1.663-1.73541.57914.42260.254-0.68563.4343-0.19144.735874.626362.1911-83.7288
211.5643-0.1392-2.27440.58760.42452.99720.2873-0.4230.3974-0.1609-0.0317-0.1771-0.87320.3662-0.28432.6292-0.15780.05492.16340.09192.536390.786560.6393-28.183
225.38625.58195.0968.10346.97987.17571.3484-1.668-0.5962-2.29290.9185-2.2171-1.541-1.1713-1.92753.0935-0.15830.51273.9510.50343.7765-23.5789-21.2982-20.4785
236.29460.78481.16021.95352.2115.8410.8528-0.80070.0026-0.28910.88981.6361-2.4291-1.9335-1.41783.31530.44190.76142.94020.84093.6495-14.2228-19.6007-23.2961
241.4959-1.9211-0.34886.98574.67494.5999-0.961-0.886-1.06650.6669-0.69551.39961.3304-0.78891.52383.0917-0.53160.64712.52510.27633.2355-8.64-53.4457-39.8832
250.6723-0.4401-0.0090.4785-0.561.62110.1654-0.79690.66990.6499-0.04950.61371.2676-1.6115-0.16713.1038-0.84430.27713.15820.45063.6047-19.5159-52.869-32.5978
262.56571.38211.72092.76212.08893.03070.6044-0.48350.24240.4351-1.03710.93141.1749-1.45380.36492.939-0.3280.28223.30110.42853.381-17.8481-52.2489-35.6262
270.8289-1.7064-0.88854.70310.86616.44890.5138-0.02460.67983.44010.10980.34350.82760.432-0.5563.1436-0.71220.68163.28330.5973.3491-1.0643-52.9718-29.7405
281.54890.00821.34156.30510.73942.8155-0.23330.6650.48890.1968-0.2279-0.0017-0.7948-0.25890.3233.09740.03350.99533.2070.25074.1567-19.8674-13.6059-24.8291
294.51490.22931.14223.54371.37060.76481.2529-0.11180.55660.1243-0.51071.2880.267-0.6076-1.09923.11610.16141.03153.17890.42583.8349-14.6757-27.24-19.4329
306.2805-0.43960.03725.40.91742.1907-0.349-1.39591.1161-0.02470.9679-2.0020.4161-1.7347-0.23682.5479-0.09280.38552.96560.11872.5363.2491-22.5595-12.8597
311.51930.97880.1531.97180.09831.36980.62660.19750.05650.7601-0.83320.6231-1.0208-0.45440.32413.92990.84110.67313.3172-0.32053.64091.035111.8288-6.5014
325.6283-3.4108-2.8099.37798.30228.48291.5736-0.56210.91831.4754-1.92030.5953-0.1041-3.56470.21392.8680.45590.7592.98270.14253.35987.251-20.997-15.1307
338.6684-0.3246-4.75896.95030.73643.14670.56671.1660.63490.53660.6816-1.37951.5099-3.3198-0.95863.95020.4420.5173.7316-0.13942.374-8.5577-18.3474-7.3865
342.6945-3.7381-1.64377.14972.5043.20260.19070.2357-0.5512-1.4037-0.29510.61020.42980.0002-0.03633.4936-0.1242-0.15752.75660.09763.128811.641-57.435-83.1746
352.78770.4918-1.4161.6784-1.29962.0592-0.33560.08690.0129-0.76480.1324-0.15010.65850.51870.05093.5437-0.091-0.05763.23950.04582.467939.6078-36.9517-96.7947
363.0763-1.0952-0.57485.18472.08413.1184-0.20270.63440.4701-1.11220.3035-0.1459-0.1072-0.277-0.1192.8303-0.1815-0.13172.66140.46292.57069.481-28.315-75.6019
373.08941.96660.06673.19122.44483.69770.0677-0.2708-0.6514-0.685-0.35281.12560.7441-1.90330.39372.867-0.1767-0.24083.37880.5693.2965-7.2711-49.8068-62.5129
381.79330.58610.51511.10610.04450.2266-0.1358-0.4242-0.3494-0.14530.74450.32840.87240.0125-0.59533.0524-0.12720.18572.96230.33462.321717.1286-57.7475-35.8951
393.6616-1.23330.68575.23620.98872.64710.45781.2078-0.804-1.64280.1270.71310.5490.1951-0.06613.6365-0.1308-0.02783.7030.36872.55024.1042-70.6944-51.7721
401.9389-0.63320.93622.5044-0.091-0.22510.25410.5513-0.1298-1.1224-0.06171.22470.5009-0.5773-0.14753.3076-0.08630.02393.63390.61532.9393-9.142-42.1352-58.1682
416.0902-1.5668-2.48821.6950.97861.9345-0.3576-0.0353-0.61790.34750.3490.44120.5823-0.29730.1772.7173-0.09280.31022.17960.11581.93234.5559-39.6207-37.4444
425.3005-2.2149-2.96772.26941.07372.5508-0.0854-0.1549-0.2190.04490.0492-0.081-0.02990.09870.11772.6688-0.15280.07111.7886-0.02171.713656.1202-50.2317-50.227
432.3728-0.3384-0.07351.2529-0.21371.74370.00960.44440.9622-0.23340.23490.0692-0.7612-0.1094-0.28043.019-0.10030.43222.02750.1052.504637.1693-8.9162-47.083
445.1891-2.81393.66672.5771-0.78584.4442-1.3978-0.98420.63141.3363-1.5507-1.2053-0.66513.20142.93343.882-0.0178-0.09714.33960.2352.890236.4844-18.5597-18.1757
458.53-1.70453.40391.9570.82918.9345-1.39-2.0901-0.03565.09720.16510.13541.10551.44351.27434.94680.36540.17213.7452-0.41062.418545.3495-28.0856-17.7072
462.5948-1.4771.15986.2887-0.09366.1719-0.7746-1.58970.17751.89370.4459-0.2843-3.02430.878-0.38674.33290.1020.0864.5228-0.10792.996136.5987-30.195-10.2048
477.3983-4.13094.12066.8205-5.46764.587-0.32090.3851.77461.024-1.3868-2.5832.51380.10371.83565.31480.8993-0.30974.15420.07123.651753.7538-31.2059-4.6473
483.1921-4.11330.40778.1575-0.40361.4895-0.0253-0.3568-0.04970.7639-0.4434-0.45950.4857-0.13020.47833.4735-0.14140.45482.69510.01842.770584.8672-89.636-71.8723
498.3059-5.35251.91734.3413-2.74513.10682.118-1.3148-4.19080.3094-2.683-3.13581.42690.82020.77224.00810.1788-0.85753.77640.37935.5766115.7949-72.0734-61.3826
501.5736-0.0872-2.06331.25420.37614.219-0.2312-0.1462-0.5627-0.2172-0.02940.00020.4521-0.45410.43933.2664-0.26140.10852.19120.04992.741353.6821-75.1321-51.2313
精密化 TLSグループ
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 149 )
3X-RAY DIFFRACTION3chain 'A' and (resid 150 through 200 )
4X-RAY DIFFRACTION4chain 'A' and (resid 201 through 238 )
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 86 )
6X-RAY DIFFRACTION6chain 'B' and (resid 87 through 179 )
7X-RAY DIFFRACTION7chain 'B' and (resid 180 through 233 )
8X-RAY DIFFRACTION8chain 'C' and (resid 3 through 224 )
9X-RAY DIFFRACTION9chain 'C' and (resid 225 through 313 )
10X-RAY DIFFRACTION10chain 'C' and (resid 314 through 437 )
11X-RAY DIFFRACTION11chain 'C' and (resid 438 through 703 )
12X-RAY DIFFRACTION12chain 'C' and (resid 704 through 1252 )
13X-RAY DIFFRACTION13chain 'C' and (resid 1253 through 1342 )
14X-RAY DIFFRACTION14chain 'D' and (resid 8 through 331 )
15X-RAY DIFFRACTION15chain 'D' and (resid 332 through 1376 )
16X-RAY DIFFRACTION16chain 'E' and (resid 2 through 60 )
17X-RAY DIFFRACTION17chain 'E' and (resid 61 through 83 )
18X-RAY DIFFRACTION18chain 'E' and (resid 84 through 90 )
19X-RAY DIFFRACTION19chain 'F' and (resid 94 through 262 )
20X-RAY DIFFRACTION20chain 'F' and (resid 263 through 354 )
21X-RAY DIFFRACTION21chain 'F' and (resid 355 through 612 )
22X-RAY DIFFRACTION22chain 'G' and (resid 7 through 22 )
23X-RAY DIFFRACTION23chain 'G' and (resid 23 through 49 )
24X-RAY DIFFRACTION24chain 'G' and (resid 50 through 86 )
25X-RAY DIFFRACTION25chain 'G' and (resid 87 through 111 )
26X-RAY DIFFRACTION26chain 'G' and (resid 112 through 153 )
27X-RAY DIFFRACTION27chain 'G' and (resid 154 through 179 )
28X-RAY DIFFRACTION28chain 'G' and (resid 180 through 197 )
29X-RAY DIFFRACTION29chain 'G' and (resid 198 through 233 )
30X-RAY DIFFRACTION30chain 'H' and (resid 6 through 48 )
31X-RAY DIFFRACTION31chain 'H' and (resid 49 through 179 )
32X-RAY DIFFRACTION32chain 'H' and (resid 180 through 212 )
33X-RAY DIFFRACTION33chain 'H' and (resid 213 through 233 )
34X-RAY DIFFRACTION34chain 'I' and (resid 3 through 114 )
35X-RAY DIFFRACTION35chain 'I' and (resid 115 through 519 )
36X-RAY DIFFRACTION36chain 'I' and (resid 520 through 703 )
37X-RAY DIFFRACTION37chain 'I' and (resid 704 through 804 )
38X-RAY DIFFRACTION38chain 'I' and (resid 805 through 906 )
39X-RAY DIFFRACTION39chain 'I' and (resid 907 through 979 )
40X-RAY DIFFRACTION40chain 'I' and (resid 980 through 1212 )
41X-RAY DIFFRACTION41chain 'I' and (resid 1213 through 1342 )
42X-RAY DIFFRACTION42chain 'J' and (resid 16 through 452 )
43X-RAY DIFFRACTION43chain 'J' and (resid 453 through 1375 )
44X-RAY DIFFRACTION44chain 'K' and (resid 2 through 12 )
45X-RAY DIFFRACTION45chain 'K' and (resid 13 through 31 )
46X-RAY DIFFRACTION46chain 'K' and (resid 32 through 55 )
47X-RAY DIFFRACTION47chain 'K' and (resid 56 through 80 )
48X-RAY DIFFRACTION48chain 'L' and (resid 94 through 292 )
49X-RAY DIFFRACTION49chain 'L' and (resid 293 through 333 )
50X-RAY DIFFRACTION50chain 'L' and (resid 334 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://pdbjlvh1.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