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- PDB-7ff9: Pseudomonas aeruginosa Virulence Factor Regulator with cAMP ligan... -

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基本情報

登録情報
データベース: PDB / ID: 7ff9
タイトルPseudomonas aeruginosa Virulence Factor Regulator with cAMP ligand and Cl(triethylphosphine)gold(I)
要素cAMP-activated global transcriptional regulator Vfr
キーワードDNA BINDING PROTEIN / auranofin / virulence / cyclic AMP receptor protein
機能・相同性
機能・相同性情報


DNA-binding transcription repressor activity / DNA-binding transcription activator activity / cAMP binding / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription / positive regulation of DNA-templated transcription / cytosol
類似検索 - 分子機能
helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site ...helix_turn_helix, cAMP Regulatory protein / Transcription regulator HTH, Crp-type, conserved site / Crp-type HTH domain signature. / : / Crp-like helix-turn-helix domain / Crp-type HTH domain profile. / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding domain signature 1. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
類似検索 - ドメイン・相同性
: / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / cAMP-activated global transcriptional regulator Vfr
類似検索 - 構成要素
生物種Pseudomonas aeruginosa PAO1 (緑膿菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2.4 Å
データ登録者Chew, B.L.A. / Luo, D.
資金援助 シンガポール, 1件
組織認可番号国
Ministry of Education (MoE, Singapore)2016-T2-2-097 シンガポール
引用ジャーナル: Comput Struct Biotechnol J / 年: 2023
タイトル: Structural basis for the inhibitory mechanism of auranofin and gold(I) analogues against Pseudomonas aeruginosa global virulence factor regulator Vfr.
著者: Zhang, Y. / Chew, B.L.A. / Wang, J. / Yuan, M. / Yam, J.K.H. / Luo, D. / Yang, L.
履歴
登録2021年7月23日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年7月27日Provider: repository / タイプ: Initial release
改定 1.12023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
改定 2.02025年3月5日Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description / Structure summary
カテゴリ: atom_site / citation ...atom_site / citation / citation_author / pdbx_entry_details / pdbx_nonpoly_scheme / struct_ncs_dom_lim
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

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集合体

登録構造単位
A: cAMP-activated global transcriptional regulator Vfr
B: cAMP-activated global transcriptional regulator Vfr
C: cAMP-activated global transcriptional regulator Vfr
D: cAMP-activated global transcriptional regulator Vfr
E: cAMP-activated global transcriptional regulator Vfr
F: cAMP-activated global transcriptional regulator Vfr
G: cAMP-activated global transcriptional regulator Vfr
H: cAMP-activated global transcriptional regulator Vfr
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)200,31264
ポリマ－190,7888
非ポリマー9,52456
水12,178676
1
A: cAMP-activated global transcriptional regulator Vfr
B: cAMP-activated global transcriptional regulator Vfr
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,30518
ポリマ－47,6972
非ポリマー2,60816
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
2
C: cAMP-activated global transcriptional regulator Vfr
D: cAMP-activated global transcriptional regulator Vfr
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)50,36618
ポリマ－47,6972
非ポリマー2,66916
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
3
E: cAMP-activated global transcriptional regulator Vfr
F: cAMP-activated global transcriptional regulator Vfr
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)49,90114
ポリマ－47,6972
非ポリマー2,20412
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
4
G: cAMP-activated global transcriptional regulator Vfr
H: cAMP-activated global transcriptional regulator Vfr
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)49,74014
ポリマ－47,6972
非ポリマー2,04312
水362
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
Length a, b, c (Å)49.738, 87.615, 104.973
Angle α, β, γ (deg.)79.039, 77.872, 75.402
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and ((resid 15 and (name N or name...
d_2ens_1(chain "C" and ((resid 15 and (name N or name...
d_3ens_1(chain "E" and ((resid 15 and (name N or name...
d_4ens_1(chain "G" and ((resid 15 and (name N or name...
d_1ens_2(chain "B" and ((resid 22 through 24 and (name N...
d_2ens_2(chain "D" and ((resid 22 through 24 and (name N...
d_3ens_2(chain "F" and ((resid 22 through 24 and (name N...
d_4ens_2(chain "H" and ((resid 22 through 24 and (name N...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1LYSLYSLYSLYSAA1511
d_12ens_1HISHISHISHISAA1915
d_13ens_1HISHISARGARGAA21 - 3717 - 33
d_14ens_1GLUGLUILEILEAA39 - 4535 - 41
d_15ens_1GLYGLYGLYGLYAA47 - 5843 - 54
d_16ens_1METMETGLUGLUAA61 - 7957 - 75
d_17ens_1GLNGLNGLUGLUAA85 - 11681 - 112
d_18ens_1LEULEULEULEUAA118114
d_19ens_1THRTHRGLNGLNAA120 - 157116 - 153
d_110ens_1PROPROTHRTHRAA159 - 173155 - 169
d_111ens_1GLNGLNGLYGLYAA175 - 178171 - 174
d_112ens_1ILEILESERSERAA180 - 184176 - 180
d_113ens_1GLUGLUGLUGLUAA186182
d_114ens_1VALVALVALVALAA188 - 203184 - 199
d_115ens_1GLYGLYGLYGLYAA205201
d_116ens_1THRTHRPHEPHEAA207 - 211203 - 207
d_21ens_1LYSLYSLYSLYSCC1511
d_22ens_1HISHISHISHISCC1915
d_23ens_1HISHISARGARGCC21 - 3717 - 33
d_24ens_1GLUGLUILEILECC39 - 4535 - 41
d_25ens_1GLYGLYGLYGLYCC47 - 5843 - 54
d_26ens_1METMETGLUGLUCC61 - 7957 - 75
d_27ens_1GLNGLNGLUGLUCC85 - 11681 - 112
d_28ens_1LEULEULEULEUCC118114
d_29ens_1THRTHRGLNGLNCC120 - 157116 - 153
d_210ens_1PROPROTHRTHRCC159 - 173155 - 169
d_211ens_1GLNGLNGLYGLYCC175 - 178171 - 174
d_212ens_1ILEILESERSERCC180 - 184176 - 180
d_213ens_1GLUGLUGLUGLUCC186182
d_214ens_1VALVALVALVALCC188 - 203184 - 199
d_215ens_1GLYGLYGLYGLYCC205201
d_216ens_1THRTHRPHEPHECC207 - 211203 - 207
d_31ens_1LYSLYSLYSLYSEE1511
d_32ens_1HISHISHISHISEE1915
d_33ens_1HISHISARGARGEE21 - 3717 - 33
d_34ens_1GLUGLUILEILEEE39 - 4535 - 41
d_35ens_1GLYGLYGLYGLYEE47 - 5843 - 54
d_36ens_1METMETGLUGLUEE61 - 7957 - 75
d_37ens_1GLNGLNGLUGLUEE85 - 11681 - 112
d_38ens_1LEULEULEULEUEE118114
d_39ens_1THRTHRGLNGLNEE120 - 157116 - 153
d_310ens_1PROPROTHRTHREE159 - 173155 - 169
d_311ens_1GLNGLNGLYGLYEE175 - 178171 - 174
d_312ens_1ILEILESERSEREE180 - 184176 - 180
d_313ens_1GLUGLUGLUGLUEE186182
d_314ens_1VALVALVALVALEE188 - 203184 - 199
d_315ens_1GLYGLYGLYGLYEE205201
d_316ens_1THRTHRPHEPHEEE207 - 211203 - 207
d_41ens_1LYSLYSLYSLYSGG1511
d_42ens_1HISHISHISHISGG1915
d_43ens_1HISHISARGARGGG21 - 3717 - 33
d_44ens_1GLUGLUILEILEGG39 - 4535 - 41
d_45ens_1GLYGLYGLYGLYGG47 - 5843 - 54
d_46ens_1METMETGLUGLUGG61 - 7957 - 75
d_47ens_1GLNGLNGLUGLUGG85 - 11681 - 112
d_48ens_1LEULEULEULEUGG118114
d_49ens_1THRTHRGLNGLNGG120 - 157116 - 153
d_410ens_1PROPROTHRTHRGG159 - 173155 - 169
d_411ens_1GLNGLNGLYGLYGG175 - 178171 - 174
d_412ens_1ILEILESERSERGG180 - 184176 - 180
d_413ens_1GLUGLUGLUGLUGG186182
d_414ens_1VALVALVALVALGG188 - 203184 - 199
d_415ens_1GLYGLYGLYGLYGG205201
d_416ens_1THRTHRPHEPHEGG207 - 211203 - 207
d_11ens_2ARGARGILEILEBB22 - 4518 - 41
d_12ens_2GLYGLYGLUGLUBB47 - 7943 - 75
d_13ens_2GLNGLNALAALABB85 - 9381 - 89
d_14ens_2VALVALSERSERBB95 - 11191 - 107
d_15ens_2GLNGLNSERSERBB113 - 115109 - 111
d_16ens_2ILEILETHRTHRBB117 - 133113 - 129
d_17ens_2LYSLYSALAALABB135 - 140131 - 136
d_18ens_2LEULEULEULEUBB142 - 155138 - 151
d_19ens_2ALAALASERSERBB161 - 184157 - 180
d_110ens_2GLUGLUVALVALBB186 - 203182 - 199
d_111ens_2THRTHRPHEPHEBB207 - 211203 - 207
d_21ens_2ARGARGILEILEDD22 - 4518 - 41
d_22ens_2GLYGLYGLUGLUDD47 - 7943 - 75
d_23ens_2GLNGLNALAALADD85 - 9381 - 89
d_24ens_2VALVALSERSERDD95 - 11191 - 107
d_25ens_2GLNGLNSERSERDD113 - 115109 - 111
d_26ens_2ILEILETHRTHRDD117 - 133113 - 129
d_27ens_2LYSLYSALAALADD135 - 140131 - 136
d_28ens_2LEULEULEULEUDD142 - 155138 - 151
d_29ens_2ALAALASERSERDD161 - 184157 - 180
d_210ens_2GLUGLUVALVALDD186 - 203182 - 199
d_211ens_2THRTHRPHEPHEDD207 - 211203 - 207
d_31ens_2ARGARGILEILEFF22 - 4518 - 41
d_32ens_2GLYGLYGLUGLUFF47 - 7943 - 75
d_33ens_2GLNGLNALAALAFF85 - 9381 - 89
d_34ens_2VALVALSERSERFF95 - 11191 - 107
d_35ens_2GLNGLNSERSERFF113 - 115109 - 111
d_36ens_2ILEILETHRTHRFF117 - 133113 - 129
d_37ens_2LYSLYSALAALAFF135 - 140131 - 136
d_38ens_2LEULEULEULEUFF142 - 155138 - 151
d_39ens_2ALAALASERSERFF161 - 184157 - 180
d_310ens_2GLUGLUVALVALFF186 - 203182 - 199
d_311ens_2THRTHRPHEPHEFF207 - 211203 - 207
d_41ens_2ARGARGILEILEHH22 - 4518 - 41
d_42ens_2GLYGLYGLUGLUHH47 - 7943 - 75
d_43ens_2GLNGLNALAALAHH85 - 9381 - 89
d_44ens_2VALVALSERSERHH95 - 11191 - 107
d_45ens_2GLNGLNSERSERHH113 - 115109 - 111
d_46ens_2ILEILETHRTHRHH117 - 133113 - 129
d_47ens_2LYSLYSALAALAHH135 - 140131 - 136
d_48ens_2LEULEULEULEUHH142 - 155138 - 151
d_49ens_2ALAALASERSERHH161 - 184157 - 180
d_410ens_2GLUGLUVALVALHH186 - 203182 - 199
d_411ens_2THRTHRPHEPHEHH207 - 211203 - 207

NCSアンサンブル:
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixベクター
1given(0.996776310486, -0.0786149854464, -0.016020952451), (0.0788702790966, 0.99675681141, 0.0159792985514), (0.0147127811578, -0.0171913632455, 0.999743962773)-0.940071066989, -33.3677087146, 50.9872810686
2given(0.999943253456, -0.00907858307419, -0.00557397501464), (-0.00901080949093, -0.999886602388, 0.0120659719037), (-0.00568288486748, -0.0120150611745, -0.999911667661)21.8420332691, 38.2325165895, 1.65638840997
3given(0.996819238447, -0.0761906327017, -0.0233750582987), (-0.0760417352251, -0.997078674047, 0.00719529464153), (-0.0238549861855, -0.00539492813095, -0.999700872454)-1.23622300925, -12.9511197463, -49.4422766802
4given(0.998609986969, 0.0393229316736, -0.0350970222517), (-0.0405013005536, 0.998617070696, -0.0335200055028), (0.033730380665, 0.0348948873051, 0.998821609828)-3.39612206333, -34.251843049, 49.3580452287
5given(0.999998693343, -0.0015137776011, 0.000567265929952), (-0.00152535603069, -0.99977833411, 0.0209989507703), (0.000535352445122, -0.0209997886144, -0.999779336792)21.8558874157, 38.4251885554, 1.78534756294
6given(0.998709090994, 0.0359525269857, -0.035882689005), (0.037971783382, -0.997635985637, 0.0572763810708), (-0.0337386311767, -0.0585649721687, -0.997713309925)-3.44214290314, -12.2364206482, -47.6128452864

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要素

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タンパク質 , 1種, 8分子 ABCDEFGH

#1: タンパク質
cAMP-activated global transcriptional regulator Vfr


分子量: 23848.521 Da / 分子数: 8 / 由来タイプ: 組換発現 / 詳細: Soaked in Cl(trimethylphosphine)gold(I)
由来: (組換発現) Pseudomonas aeruginosa PAO1 (緑膿菌)
株: PAO1 / 遺伝子: vfr, PA0652 / 発現宿主: Escherichia coli (大腸菌) / 株 (発現宿主): T1R / 参照: UniProt: P55222

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非ポリマー , 5種, 732分子

#2: 化合物
ChemComp-CMP / ADENOSINE-3',5'-CYCLIC-MONOPHOSPHATE / CYCLIC AMP / CAMP


分子量: 329.206 Da / 分子数: 8 / 由来タイプ: 合成 / 式: C10H12N5O6P / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物...
ChemComp-AU / GOLD ION


分子量: 196.967 Da / 分子数: 31 / 由来タイプ: 合成 / 式: Au / タイプ: SUBJECT OF INVESTIGATION
#4: 化合物
ChemComp-CL / CHLORIDE ION


分子量: 35.453 Da / 分子数: 14 / 由来タイプ: 合成 / 式: Cl / タイプ: SUBJECT OF INVESTIGATION
#5: 化合物 ChemComp-SO4 / SULFATE ION


分子量: 96.063 Da / 分子数: 3 / 由来タイプ: 合成 / 式: SO4
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 676 / 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: 2.24 Å3/Da / 溶媒含有率: 45.2 %
解説: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 2.6M Ammonium Sulphate, 0.1M Bicine pH 9.0

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データ収集

回折平均測定温度: 200 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Australian Synchrotron / ビームライン: MX1 / 波長: 0.9537 Å
検出器タイプ: DECTRIS EIGER2 X 9M / 検出器: PIXEL / 日付: 2019年9月22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: 0.9537 Å / 相対比: 1
反射解像度: 2.4→46.53 Å / Num. obs: 121837 / % possible obs: 98.44 % / 冗長度: 3 % / CC1/2: 0.994 / Net I/σ(I): 10.68
反射 シェル解像度: 2.4→2.486 Å / Num. unique obs: 6402 / CC1/2: 0.807

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解析

ソフトウェア
名称バージョン分類
Coot0.8.9モデル構築
PHENIX1.19.2_4158精密化
HKL-3000データ削減
Aimlessデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 2OZ6

2oz6


解像度: 2.4→46.53 Å / 交差検証法: FREE R-VALUE / σ(F): 78.97 / 位相誤差: 34.3337
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2927 6404 5.26 %
Rwork0.2641 115433 -
obs0.2658 121837 93.86 %
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 mean: 33.43 Å2
精密化ステップサイクル: LAST / 解像度: 2.4→46.53 Å
タンパク質核酸リガンド溶媒全体
原子数11618 0 236 676 12530
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.010311967
X-RAY DIFFRACTIONf_angle_d1.580516182
X-RAY DIFFRACTIONf_chiral_restr0.09491912
X-RAY DIFFRACTIONf_plane_restr0.02042033
X-RAY DIFFRACTIONf_dihedral_angle_d11.00111763
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.29267141999
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.717204896452
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.37287727875
ens_2d_2CX-RAY DIFFRACTIONTorsion NCS1.01976976377
ens_2d_3CX-RAY DIFFRACTIONTorsion NCS0.98077501408
ens_2d_4CX-RAY DIFFRACTIONTorsion NCS1.12562133572
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.33292800.31835879X-RAY DIFFRACTION90.5
2.44-2.490.35942900.31465944X-RAY DIFFRACTION90.25
2.49-2.530.36223090.31935691X-RAY DIFFRACTION89.68
2.53-2.590.3733120.31375890X-RAY DIFFRACTION89.9
2.59-2.640.3263530.29915832X-RAY DIFFRACTION89.17
2.64-2.70.2552610.30645770X-RAY DIFFRACTION89.9
2.7-2.770.29513160.2955860X-RAY DIFFRACTION88.57
2.77-2.850.28362540.28545645X-RAY DIFFRACTION88.23
2.85-2.930.33842940.285746X-RAY DIFFRACTION87.22
2.93-3.020.31122790.2845619X-RAY DIFFRACTION87.91
3.02-3.130.31842610.27085784X-RAY DIFFRACTION89.15
3.13-3.260.28832670.26145921X-RAY DIFFRACTION91.86
3.26-3.410.29493320.26135891X-RAY DIFFRACTION90.69
3.41-3.580.2663120.25425915X-RAY DIFFRACTION90.03
3.59-3.810.2753160.25165856X-RAY DIFFRACTION90.06
3.81-4.10.26933120.23515705X-RAY DIFFRACTION89.03
4.1-4.520.23643200.21115773X-RAY DIFFRACTION88.71
4.52-5.170.24192910.235622X-RAY DIFFRACTION87.19
5.17-6.510.34113130.28345549X-RAY DIFFRACTION85.45
6.51-46.530.32752620.26256011X-RAY DIFFRACTION92.25
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)
12.00317125859-0.1997388164390.6955955803862.99039576308-0.8455629040370.487619387273-0.15978522314-1.02985341736-0.2117643599570.9720317791140.02136059888310.860107306919-0.0350289709005-0.8089843557120.09934102057180.01505189645230.07769914155880.02829898766490.6848317279740.05639112197640.403093208138-11.286411866917.2695834814-18.1882527273
23.53217799932-0.145373682431-0.8161857734971.32522669356-0.4306418235321.64188555515-0.0821691254509-0.06058305297510.1338167745810.1025854713410.05673832389370.069951766416-0.146405132026-0.0798240156473-0.01018407154790.1534039789760.0289888039698-0.03060512168080.3145299357260.04030446521290.218834116299-1.1511388790217.0778524398-21.5435630904
32.113891924240.635805550465-0.4703386545173.91756865942-1.114688342192.468553877840.0601854483755-0.199661423806-0.0627720208476-0.222636506702-0.02130298342310.1010470044380.391434374444-0.131263508087-0.02143384400840.2203231523350.0136854233012-0.03000328126740.3473200994070.07611877881830.176298489749-1.191548274890.0619622301134-38.3988177982
41.45792334769-0.28209482546-0.7858648257962.695754976120.3769477056590.5805225044990.062695614654-1.138251810670.2495147958282.10496419534-0.556837820232-0.3223532448710.1519492157310.684210444618-0.152203749014-0.2035931377560.0819557553701-0.3435918268890.592085209374-0.007435248747150.42552940985227.068034270323.7825553186-18.373652388
53.31179314631-0.6697917403920.1397054943673.003070541210.7534976014492.06096681667-0.0596668632933-0.138787362099-0.01746275699570.1321311008580.0675359647226-0.1065437949980.05261087805890.1540927817010.0188657448980.12180994834-0.00928512759957-0.04416998510040.3206661342770.0247086716540.28441738667717.09825614621.9712387189-22.1978252737
60.115874758174-0.2300426749140.3683083324982.710315322410.4992874771080.590580637479-0.0075324124052-0.06423969608230.04028736735430.2325579274640.2232857441590.580619684967-0.410737253691-0.4197584773950.0231089472750.484649199342-0.0198274123454-0.002088604001940.4231752322330.01104075402310.27373931614112.50336592931.7684254854-46.423718835
71.66450532693-0.422482393513-0.7101942409193.89103254663-0.401927119932.128767027830.1693580812660.199858776310.232006389764-0.941939835794-0.399494227743-0.0375565083951-0.8068224142050.5811066360.03467608869810.536303652079-0.005407260192920.01753541542040.465694508476-0.05717995926070.28426011179818.222122968826.7711834431-51.6241240055
82.342507155250.5324049173240.2798854944142.293123112560.3531660789382.832906465960.159270006377-0.08139869411290.1481907519170.0978091164123-0.1136640819290.0868675124414-0.221577373751-0.15772120393-0.04506686260620.1177311040210.05054000342540.02068732170770.3842426298940.03971809765930.181287715788-8.68946419974-16.996931978727.7470927356
92.403125094990.4078074390460.1108816467230.396138924558-0.6492321564621.663670594670.045615211794-0.5049169493390.01856335126250.183408686507-0.1560549098670.0962408515043-0.189164343742-0.187261008112-0.05983198072750.1934536772270.02547673508820.01881849117670.4619281663030.0134186216960.2125089087431.05523085643-16.961060173632.9343744044
101.03778466234-0.001700857257180.557349642232.40582662216-0.555710324891.27583723806-0.0579579361181-0.00716059357852-0.149657877680.2833179197720.1545145051080.07391590617720.341556882228-0.320686195551-0.04843515392660.276919244663-0.005745370708460.00434867469460.3660924212180.05551547297210.149728305086-1.2823750972-34.360722665512.1835891852
112.568796725970.937186084501-1.805762912483.11615763935-1.379095259221.788520400010.620904420067-0.956955871265-0.09001590762870.741601616275-0.162384702253-0.659757118269-0.06922745361920.478522591321.880382061230.1470115923920.0184897152033-0.07205421408560.6868447605430.03430651520320.29814675140225.4505104435-12.405892859531.6644187652
123.062194580710.2456489401790.2684238251491.04008954558-0.3971300430982.271410664740.108134708432-0.21799573307-0.03351725241980.0969744677464-0.0451453761363-0.08759172249020.0606761085208-0.0297078574251-0.03168274035730.1350736310280.009644410614110.005305122839580.3837459938030.01372471016120.24578200166914.8933485969-12.698190262128.6687473058
130.6190319475520.09281299952280.1498479818523.01171726387-1.55593781841.22007900659-0.0178361754132-0.09936727501080.1331419640910.0631339548330.1556937089720.042422147663-0.09937760318010.251368298868-0.05049689540070.328864086133-0.05536520837340.001542082403090.409161832599-0.05110765981190.23044987453515.6483539873-3.579141847091.35977413765
143.144627677880.449256686749-0.5171369073382.570940591690.7475656823142.248922012310.08059983336850.125131012555-0.1281599771690.0285035947191-0.1077221816860.139423145010.208940183619-0.0697149591361-0.043626302670.0791965669832-0.0219457409828-0.02084138938890.4602605147670.06320736367160.18239595298814.806788611821.024458661124.5757470097
150.520028203668-0.11922158094-0.1463115885212.428384500521.084323701661.967403761460.06941847336410.1134139989970.0760993905583-0.0597305774567-0.0392813884456-0.0618179268594-0.40761399458-0.0173456691817-0.04299285458720.163524945553-0.0524767692063-0.03091652598060.3948527795290.07459868766190.19469030462622.514514435130.926109243531.1526401952
162.025696063810.709005916223-0.2016009782312.73545862061.530721492933.011580802610.2763053016880.406277961265-0.41760390142-0.3422573523850.00825766687054-0.5709355047780.6811378937220.1897257984210.248538413874-0.0103618362314-0.14084048511-0.002746273158090.4992341373030.04021799798460.24745827443447.51317860315.389534757425.236925229
174.48274282974-0.114441130586-0.7306104059873.184640790490.4750444381731.83970951901-0.03019492316650.574728749785-0.0330997108893-0.3396430319750.07338810537990.0164492869308-0.09411099675010.00180533149963-0.01851539151020.187918961782-0.0601671766094-0.0324827649190.4156496701150.01739292755440.23403882901838.048719634116.317484044822.8429271764
184.69401099848-2.688645983011.950046145753.31453725372-1.041190374761.569639600960.37942906380.00883396880162-0.399559464368-0.9066409150850.2674298853880.5582512995680.1547406318570.3970547105780.29644882950.3956495196070.02558589339170.02503076915470.686614246020.04921970918790.29432152134630.425225243113.632678950547.9042912228
193.13322999007-0.944091888475-1.450571997823.26475375881.864086550961.35417180690.202386971221.458020016330.0373506631985-0.4946022001130.4008069965320.1573543291010.248292392627-0.9433540298120.08872575388461.42743205444-0.2514092952850.2965900826271.266296194570.2700825529540.6492742824633.3100483132-4.1429189574748.7614076407
202.89392370173-0.6836939590792.130530661323.34096139481-0.7211406139571.51668392357-0.523713848230.7733871936910.340549044557-0.2693929588770.329728985048-1.166532001180.3016738119461.27652997334-0.1015010546060.3662142279610.1873016480120.09936216686130.506564392821-0.05908196955130.168566733141.16890346529.8918998893646.3940699082
214.87008593883-2.683253176111.388756621584.60291143654-1.209594316961.10410150555-0.5835898731370.2422903253860.4589646863761.42729411858-0.211437421535-1.03639381353-0.2159017319630.720677049923-0.4518339114860.585667096868-0.0476526855599-0.06054966570750.792595482941-0.1328798661860.35914264724940.49466419714.562075325756.1555963089
223.24871596273-1.35158952633-0.6154934026970.7825092474320.2924773358620.3040828879260.292091468046-0.5511487616790.04543983963890.468536546842-0.161339804229-1.138887148420.6612221195690.366873214535-0.1429753885190.7000023415620.0105046334808-0.0604187464330.9737685161660.01929177889980.69251096771337.95470753953.5297207563855.6422930272
230.765815470960.6833281045160.1659263964262.8246143329-0.01673207689840.579048821555-0.2025031472781.147871913620.298211816054-1.323894696150.04408226974940.1538212732770.1787155384610.3575975871180.0207198439290.40593252556-0.0532579784354-0.1192028448381.198255437210.1363087946730.604133011705-12.8532833117-26.1454072575-39.2913800961
242.54590990353-0.928335687832-0.1674902499472.92176806908-0.2597811301052.120427567660.6599736865960.3575845419840.169973927295-0.908848672533-0.316647355724-0.474746353112-0.0184082896519-0.7250915925810.01237586991850.174824067627-0.0235502835991-0.05398054542270.3406058995350.03185533311090.167538899144-14.1237687168-33.0077725876-24.2722256213
250.8256521624890.310291613853-0.1092776905261.743436321050.1516764370252.112114230170.1607038243790.07644937828880.006197733958180.00959501711966-0.1104882193670.06643676728010.03772596071350.12544888147-0.06523309908820.0928225161398-0.02150351636410.003386163342990.3276790628060.02264856769670.183128928226-6.15877496755-28.4477026037-24.0030611579
262.355793747170.703039475897-0.3617753268070.994645115224-0.2334285615072.27576255275-0.1009561218960.258927951461-0.4421576678530.759180929041-0.2342368120780.09077545741970.5217482714-0.403042811581-0.7496228469880.104430279223-0.0477217594888-0.1198652350130.5285564305390.133284793120.107676071785-7.47978841869-34.8291360427-25.0774623203
271.44518526689-0.3146718023680.227109341073.242004087420.8111555156842.040399407890.3937025028610.3832081645120.140312625559-0.73534089024-0.04292665910410.0121256445024-0.6245677061780.0685665228249-0.02322888631240.198927273469-0.0684470054918-0.009338941600620.3948909130720.0280409936590.188842654673-6.37935731435-32.9746078905-40.9616155626
281.28433596061-0.3200581592270.6340133510623.948629740112.99945609452.53457321632-0.01178935931940.1688964547320.161696592737-1.45424769785-0.412116246114-0.421846622683-1.15819404334-0.148893565674-0.160648156668-0.293764705057-0.1854463278910.03612383348110.4360598449020.08752465910680.198446166485.96723442462-27.3567090579-25.3824890437
292.1108568897-0.06203910777110.3820173516661.847398698590.8427132204313.146111610910.5032560405320.01403631239770.442673157921-0.4186264600930.455305109829-0.156982627678-0.708979001177-0.1176207679030.2874086778990.2825096353140.0333026916940.03741749929670.3632980311520.04055367845770.1606683773143.9849885021-17.2631374088-12.1054805522
300.5887752390051.13386910447-0.3284758875552.54993269203-0.3051973876940.361888589488-0.1195469468480.5273509994760.408479675565-0.6685580369730.2932551679240.628725353042-0.279577062696-0.1483618960050.5276064512630.3817049562770.08327169002460.01158690209770.3508837036710.1023049582120.152450576168-3.38297288782-7.57173139225-18.9976118727
311.52221180487-1.17916979314-1.099821911915.074070106450.08224001171322.81164534423-0.25367153347-0.216631436873-0.2178530360820.8684223968621.03481157660.754794486220.56125780069-1.504163100020.006763812879220.375010135323-0.1083913737640.02854459746650.5389745686270.1117630279930.211372719687-6.27248524216-21.3098557106-7.73401581237
321.120147248380.1506354399050.5622003908921.548708814620.7099041560691.081674780170.284048091011-0.02609298740730.06522552715290.0693929832778-0.09497563406360.196911322162-0.958515597189-0.266360318413-0.01853281624670.3991120175250.003272390587620.04167148324010.3590636511560.04463000816380.172981143776-1.44242512048-9.55932421605-6.25976375027
334.050208956140.4184481394670.3389553061731.702115910550.4903026206951.756267974290.05113490754440.409558632854-0.18355905543-0.0904898776150.0437234829981-0.0450058769786-0.07767284729670.10828941536-0.02830564990720.108635243469-0.00786562912686-0.003891199293660.3348782816570.03446035457270.21551295474516.5198763456-34.6680586001-26.9481256805
341.51277071927-0.569565281708-0.04503080736452.588167425-1.096966032011.177978344310.0109274482452-0.255822953038-0.0473175674550.07706067876-0.0483795825314-0.09103057924470.007584438271780.0865939898641-0.01611093865270.2721998877450.0327271568918-0.03914468902150.4293010428280.06085786326590.22063407539315.560909217-43.6715347808-0.139195569451
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 39 )AA13 - 391 - 27
22chain 'A' and (resid 40 through 141 )AA40 - 14128 - 126
33chain 'A' and (resid 142 through 212 )AA142 - 212127 - 197
44chain 'B' and (resid 13 through 39 )BC13 - 391 - 27
55chain 'B' and (resid 40 through 139 )BC40 - 13928 - 124
66chain 'B' and (resid 140 through 173 )BC140 - 173125 - 158
77chain 'B' and (resid 174 through 212 )BC174 - 212159 - 195
88chain 'C' and (resid 13 through 96 )CE13 - 961 - 81
99chain 'C' and (resid 97 through 141 )CE97 - 14182 - 126
1010chain 'C' and (resid 142 through 212 )CE142 - 212127 - 197
1111chain 'D' and (resid 14 through 39 )DG14 - 391 - 26
1212chain 'D' and (resid 40 through 141 )DG40 - 14127 - 128
1313chain 'D' and (resid 142 through 211 )DG142 - 211129 - 198
1414chain 'E' and (resid 15 through 96 )EI15 - 961 - 79
1515chain 'E' and (resid 97 through 211 )EI97 - 21180 - 194
1616chain 'F' and (resid 22 through 54 )FK22 - 541 - 33
1717chain 'F' and (resid 55 through 139 )FK55 - 13934 - 115
1818chain 'F' and (resid 140 through 155 )FK140 - 155116 - 131
1919chain 'F' and (resid 156 through 166 )FK156 - 166132 - 142
2020chain 'F' and (resid 167 through 184 )FK167 - 184143 - 160
2121chain 'F' and (resid 185 through 197 )FK185 - 197161 - 173
2222chain 'F' and (resid 198 through 212 )FK198 - 212174 - 188
2323chain 'G' and (resid 13 through 25 )GM13 - 251 - 13
2424chain 'G' and (resid 26 through 39 )GM26 - 3914 - 27
2525chain 'G' and (resid 40 through 77 )GM40 - 7728 - 65
2626chain 'G' and (resid 78 through 96 )GM78 - 9666 - 81
2727chain 'G' and (resid 97 through 115 )GM97 - 11582 - 100
2828chain 'G' and (resid 116 through 141 )GM116 - 141101 - 126
2929chain 'G' and (resid 142 through 157 )GM142 - 157127 - 142
3030chain 'G' and (resid 158 through 173 )GM158 - 173143 - 158
3131chain 'G' and (resid 174 through 185 )GM174 - 185159 - 170
3232chain 'G' and (resid 186 through 212 )GM186 - 212171 - 197
3333chain 'H' and (resid 22 through 141 )HO22 - 1411 - 116
3434chain 'H' and (resid 142 through 211 )HO142 - 211117 - 186

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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