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- PDB-7zg5: The crystal structure of Salmonella TacAT3-DNA complex -

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基本情報

登録情報
データベース: PDB / ID: 7zg5
タイトルThe crystal structure of Salmonella TacAT3-DNA complex
要素
  • (tacAT3 DNA operator) x 2
  • Acetyltransferase
  • DUF1778 domain-containing protein
キーワードTOXIN / Toxin-antitoxin system / Salmonella / Acetyltransferase / Conditional cooperativity
機能・相同性
機能・相同性情報


transferase activity / regulation of DNA-templated transcription
類似検索 - 分子機能
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Ribbon-helix-helix / Acyl-CoA N-acyltransferase
類似検索 - ドメイン・相同性
: / COENZYME A / DNA / DNA (> 10) / Acetyltransferase / DUF1778 domain-containing protein
類似検索 - 構成要素
生物種Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
手法X線回折 / シンクロトロン / 分子置換 / 解像度: 2 Å
データ登録者Grabe, G.J. / Morgan, R.M.L. / Helaine, S.
資金援助 英国, European Union, 4件
組織認可番号国
Medical Research Council (MRC, United Kingdom)MR/M009629/1 英国
European Research Council (ERC)757369European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 英国
Wellcome Trust202926/Z/16/Z 英国
引用ジャーナル: Nat.Struct.Mol.Biol. / 年: 2024
タイトル: Molecular stripping underpins derepression of a toxin-antitoxin system.
著者: Grabe, G.J. / Giorgio, R.T. / Wieczor, M. / Gollan, B. / Sargen, M. / Orozco, M. / Hare, S.A. / Helaine, S.
履歴
登録2022年4月1日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02023年10月11日Provider: repository / タイプ: Initial release
改定 1.12024年3月27日Group: Database references / カテゴリ: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
改定 1.22024年4月3日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title
改定 1.32024年4月10日Group: Database references / カテゴリ: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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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: Acetyltransferase
B: Acetyltransferase
C: DUF1778 domain-containing protein
D: DUF1778 domain-containing protein
E: tacAT3 DNA operator
F: tacAT3 DNA operator
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)68,54015
ポリマ－66,1926
非ポリマー2,3489
水2,324129
1


  • 登録構造と同一
  • 登録者・ソフトウェアが定義した集合体
  • 根拠: native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-135 kcal/mol
Surface area29800 Å2
手法PISA
単位格子
Length a, b, c (Å)79.617, 120.096, 172.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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要素

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タンパク質 , 2種, 4分子 ABCD

#1: タンパク質 Acetyltransferase / GNAT family N-acetyltransferase / N-acetyltransferase / Putative acetyltransferase / TacT3 toxin


分子量: 19090.840 Da / 分子数: 2 / 変異: Y143F / 由来タイプ: 組換発現 / 詳細: Y143F
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
遺伝子: A2O69_14710, A3104_08525, A3111_02365, A3122_05715, A3146_07085, A3S30_20570, A3T81_15835, A3U32_19315, A3V03_13160, A3V89_13630, A3W57_15915, A3W75_13520, A3W86_09800, A3X15_14395, A3X55_ ...遺伝子: A2O69_14710, A3104_08525, A3111_02365, A3122_05715, A3146_07085, A3S30_20570, A3T81_15835, A3U32_19315, A3V03_13160, A3V89_13630, A3W57_15915, A3W75_13520, A3W86_09800, A3X15_14395, A3X55_09260, A3Y76_11330, A3Z96_17730, A4J27_06855, A4N07_06735, A4O05_06540, A4R48_05595, A6D61_06495, A9C21_11525, A9T39_06955, A9U46_17515, A9U64_03850, AAA76_13150, AAB27_19890, AAB39_07250, AAB79_09875, AAC08_00420, AAC35_15875, AAC42_08845, AAC44_05970, AAC95_11790, AAC98_08180, AAK29_13035, AAP89_06290, AAQ24_13230, AB424_06630, ABO94_10350, ABP87_20380, ADQ28_09230, ADQ45_03525, AE787_08375, AF480_02650, AF488_02445, AF489_05145, AF497_15340, AGC55_04185, AGM99_07505, AGQ32_07045, AH984_01035, AHN93_09010, AIC76_09285, AKH62_10520, AKH68_10580, AKI16_02015, AL144_10105, AL151_10950, AL166_11665, AL168_09635, AL170_09510, AL174_03655, AL184_10950, APY91_06225, AQ530_13930, AS118_08370, AT354_02285, AU613_08485, AU805_10975, AU830_04485, AU839_11895, AU951_07445, AU965_16560, AVA38_07605, AVB77_13980, AVB94_15035, AVC05_01920, AVC09_03465, AVD08_11675, AVD75_12175, AVD94_11625, AVL02_10280, AVL16_05965, AVM19_04730, AWT30_06955, AXM10_11690, AXM23_13930, AXR84_07880, AXU58_02150, AXX99_11930, B1265_07265, B1398_23385, B1642_13580, B1B86_06045, B1B89_02010, B1I91_06440, B1P38_03325, B1Q82_05910, B2E31_15360, B4V59_13460, B4W90_04250, B5A40_05340, B6362_07445, B6G98_04770, B6M25_12980, B6M43_01870, B7071_02280, B7890_10645, B7J30_02750, B7Q27_07260, B8Y16_10555, B8Y36_04530, B8Z46_07685, B9653_20405, B9C61_09950, B9C71_14620, B9C90_09640, B9C91_13400, B9C96_07470, B9M14_11835, B9O84_04625, B9U29_15940, BBQ66_03420, BEL47_20970, BGP52_08870, BIC00_01965, BIC01_05330, BIC03_09930, BIC13_10285, BK110_07455, BKM50_12355, BLB03_01740, BMS46_04300, BMU56_05250, BSC80_02300, BSD55_06335, BZ203_09215, BZ210_07060, BZG47_06310, BZN20_02445, BZZ88_18440, C4E88_02445, C5U54_02150, C5W43_12245, CA117_08410, CB102_08185, CB161_12015, CB198_02180, CB380_14500, CB383_01935, CB416_07355, CB530_05450, CB535_13640, CB570_08575, CB646_10705, CB657_09085, CBH20_06435, CBM40_20070, CBM67_16515, CBM76_14910, CBN77_16785, CBO42_11245, CBR08_04950, CBU32_07665, CBZ90_11485, CC403_06280, CC453_06265, CC594_15440, CC652_14675, CC725_04865, CC886_14180, CC918_07945, CC944_02215, CC971_01735, CCF93_10575, CCP17_12420, CCW27_01035, CD48_09215, CD977_05545, CDJ75_04635, CDT37_10325, CDZ72_03910, CE355_06180, CE615_05710, CE70_11930, CE806_07385, CE87_05355, CE896_10245, CEC46_10535, CEC56_05725, CED07_07405, CEQ70_02125, CER78_09050, CET98_05350, CEY64_12815, CFB16_10680, CFB28_09520, CFE76_07290, CFE79_02120, CFF58_10820, CFF59_05970, CFJ48_10970, CGG73_06885, CHN22_06165, CI444_05360, CIX60_02145, CJC42_03195, CPR79_16280, CPS79_11185, CPX68_05100, CQE35_07680, CQO33_16090, CR370_08455, CRB02_05340, CSG22_12020, CTJ81_12735, CVR97_12650, D3147_08940, D3174_07820, D3F31_20020, D3T68_17985, D3Y48_07440, D4361_09990, D4369_10995, D4380_01880, D4387_15140, D4422_12965, D4E62_16105, D4E68_14820, D4E74_13085, D4X64_15240, D4Y62_17435, D5823_15645, D5949_23340, D5B48_13110, D5C67_12005, D5C71_16355, D5N86_08970, D5N95_10230, D5O82_16440, D5P17_16530, D5X47_15185, D5Y28_18520, D6360_15430, D6367_13695, D6371_04230, D6373_15865, D6395_13525, D6421_15010, D6422_15625, D6J79_16905, D6K10_25570, D6P67_17865, D6Q64_15695, D6S43_13590, D6T00_01880, D6T40_09010, D7F20_20100, D7H43_13140, D7O44_15935, D8Q90_16805, D8S24_11150, D9O84_11660, DD95_05355, DJ388_12295, DJ702_05335, DK061_11060, DK631_03160, DK641_12245, DK642_13480, DK689_12875, DK696_12630, DK698_11875, DKJ10_12870, DKR95_21490, DKS55_05145, DKU45_05690, DKU57_07335, DKU80_06725, DLB14_13735, DLB57_11890, DLB93_11425, DLR28_16975, DM322_06960, DMI89_25655, DMO92_02670, DMV40_12195, DMZ93_26675, DN165_11055, DN204_16500, DN359_23735, DNB97_00775, DNL62_15760, DNM27_05590, DNU59_05715, DNV08_01875, DNV12_09940, DNV30_14235, DNY92_13980, DNZ37_15375, DO350_06855, DO533_06050, DO585_16180, DO640_14410, DO698_08950, DO766_06390, DO828_16965, DO960_09160, DOC60_02105, DOH72_07130, DOI32_13580, DOI92_13210, DOJ39_17520, DOJ91_12145, DOQ54_06625, DOQ88_13030, DOR12_06235, DOV43_10320, DOW25_12865, DP680_15120, DPB42_03780, DPB45_13780, DPB48_08570, DPB57_07290, DPD91_09220, DPD95_09935, DPD99_23550, DPF41_13030, DPF68_13810, DPJ93_05515, DPK32_07545, DPK79_14260, DPL02_04340, DPP94_15975, DPP97_15415, DPS76_00440, DPT18_14130, DPU20_13855, DPY58_11745, DQ848_11335, DQ947_01880, DQ951_13955, DQC39_17415, DQC52_23390, DQD03_08180, DQD22_04750, DQE65_01875, DQK42_05460, DQQ98_08490, DQR10_25350, DQR61_13365, DQS14_11730, DQY10_10410, DQZ46_12325, DQZ56_08295, DR982_12275, DRL45_08460, DRM14_13595, DRM16_12360, DRR75_02370, DRT38_02095, DRT61_15355, DRT65_10140, DRV05_05570, DRW84_08295, DRX66_12300, DS270_13440, DS296_06505, DS451_14735, DS453_11540, DS521_04860, DS619_14375, DSF69_15770, DSF94_01875, DSG41_06680, DSM38_13920, DSN15_14610, DSR36_07530, DTE73_08970, DTF68_01875, DTG22_06850, DTG27_07270, DTW13_15655, DTW14_17675, DTW26_10525, DU071_02620, DU223_03775, DU657_08025, DU821_15060, DU879_12775, DU924_00430, DUQ28_15105, DUQ56_12120, DUQ92_16070, DUR36_05660, DUW10_17140, DUW48_07425, DVF14_10520, DVF88_05805, DVG01_14880, DVZ53_02690, DWU22_21650, DY580_03860, DYM27_25875, DYS82_16110, DZG11_12860, E0584_17725, E0595_12520, E0935_16805, E0989_11820, E0M34_00770, E0U75_12350, E0V94_13550, E1A11_13990, E1A20_08715, E5196_10530, E6W45_11290, EBB93_08225, EBC01_14215, EBD14_10775, EBD99_16245, EBK21_12495, EBL31_10765, EBO41_07985, EBP31_13400, EC404_10185, EC52_10650, ECA50_06355, ECC89_10360, ED424_12910, ED467_14455, EDL18_12335, EEK73_07615, EEQ30_03190, EER35_13455, EGL32_13215, EGN81_14320, EGU67_16280, EGU98_01815, EHB09_17685, EHB24_06860, EHB55_04625, EHC98_13055, EIE48_07335, EIW53_10865, EJI18_11855, EJO08_15295, EJO98_03745, EKA25_05275, EL822_10545, ELO47_06300, ELR28_12910, ELS01_13730, EM832_14630, EM840_15510, EMN66_11055, EMY79_07110, EO190_01820, EP115_08910, EP446_17725, EPB30_04875, EPH81_13125, EQG93_17545, EQG94_14990, ERM04_12360, EU349_14435, EU873_14810, EUB95_06180, EUQ56_12620, EUQ65_14085, EUQ74_12140, EUS13_11340, EVY71_02270, EW905_11445, EWB18_13125, EWE52_09515, EWJ47_12360, EWZ09_10265, EXA47_14060, EXB31_10305, EXB41_12245, EYA29_09815, EYJ91_01000, F0D96_04670, F2O93_06050, F2P00_05765, F3Q46_12455, F3Q59_03865, F3Q88_17410, F3Q97_01745, F3R12_04520, F3R61_14650, F3R63_08825, F9G02_11745, F9O44_07395, FE758_05780, FEM52_10645, FGZ46_12865, FJM64_15875, FL833_14220, FQC24_10790, FQD13_05150, GCH31_04025, GCQ81_09835, GCZ80_06975, GEZ01_15490, GW08_02135, JO10_05360, KP44_07640, LZ63_05160, NG02_08975, NG06_24275, NG18_05800, NU83_05230, QA89_10955, QB40_04985, R035_04270, RJ78_02450, SAMEA4398682_01021, SE14_03092, Y934_04800, YG50_06085, YT65_12255, Z700_09660, ZT09_11460, ZT28_14425, ZT74_12940, ZT89_06430, ZU86_13060, ZU92_03155, ZV33_12500, ZV34_13970, ZV38_09350, ZV58_11905, ZV70_14285, ZV78_10390, ZW74_09615, ZX03_03830, ZY23_09620, ZY27_14455, ZY40_09835, ZY51_10295, ZZ18_13325, ZZ43_10110, ZZ77_05435, ZZ79_07510
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A0F7DJC6
#2: タンパク質 DUF1778 domain-containing protein


分子量: 10343.004 Da / 分子数: 2 / 由来タイプ: 組換発現
由来: (組換発現) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
遺伝子: A3104_08520, A3S30_20565, A3T81_15830, A3U32_19310, A3V03_13155, A3V89_13625, A3W57_15910, A3W75_13515, A3X15_14390, A3X55_09255, A3Y76_11325, A4N07_06740, A4O05_06535, A4O41_11245, A4R48_ ...遺伝子: A3104_08520, A3S30_20565, A3T81_15830, A3U32_19310, A3V03_13155, A3V89_13625, A3W57_15910, A3W75_13515, A3X15_14390, A3X55_09255, A3Y76_11325, A4N07_06740, A4O05_06535, A4O41_11245, A4R48_05600, A6D61_06490, AAA76_13145, AAB27_19885, AAB79_09870, AAC35_15870, ADQ28_09225, AF497_15335, AGM99_07500, AHN93_09005, AIT36_04960, AKH62_10515, AL144_10100, AL168_09630, AL184_10945, AQ530_13925, AU613_08480, AVA38_07600, AVC05_01915, AVL16_05970, AWT30_06960, AXX99_11925, B1265_07260, B1398_23380, B1642_13575, B1P38_03320, B2E31_15355, B4V59_13455, B4W90_04245, B6362_07440, B7Q27_07255, B8Y16_10550, B8Z46_07680, B9C90_09635, B9C96_07465, B9M14_11830, B9O84_04620, BBQ66_03415, BG493_04765, BIC00_01970, BIC13_10280, BK110_07450, BKM50_12350, BMS46_04295, BMU56_05245, BZ203_09210, BZZ88_18435, C5W43_12240, CA117_08405, CAC56_04740, CAC59_04965, CB102_08180, CB119_03925, CB198_02175, CB380_14495, CB535_13635, CB570_08570, CB646_10700, CBM67_16510, CBM76_14905, CBZ90_11480, CC339_06035, CC403_06275, CC453_06260, CC652_14670, CC971_01740, CCP17_12415, CDZ72_03905, CE70_11925, CED07_07400, CEQ70_02130, CFF58_10815, CFF59_05965, CHN22_06160, CIX60_02150, CPS79_11180, CQO33_16085, CSG22_12015, CVR97_12645, D4361_09985, D4387_15135, D4422_12960, D5823_15640, D5N86_08965, D5N95_10225, D5O82_16435, D5P17_16525, D5X47_15180, D5Y28_18515, D6422_15620, D6J79_16900, D8S24_11145, DLB93_11420, DLR28_16970, DMI89_25650, DMO92_02665, DN165_11050, DNB97_00770, DNM27_05585, DNZ37_15370, DO533_06045, DP680_15115, DPB42_03775, DPD91_09215, DPF41_13025, DPF68_13805, DPS76_00435, DQD22_04755, DQR44_14010, DRM14_13590, DRT38_02100, DRT61_15350, DRV05_05565, DSF94_01880, DSG41_06675, DTF68_01880, DU071_02615, DU223_03770, DU657_08020, DU879_12770, DUV75_06695, DWU22_21645, DY580_03855, DYM27_25870, E0935_16800, E1A11_13985, E6W45_11285, EBD14_10770, EBK21_12490, EC404_10180, EEQ30_03185, EER35_13450, EHB09_17680, EL822_10540, ELS01_13725, EPB30_04880, EQG93_17540, EVY71_02265, EW905_11440, F0D96_04665, F2P00_05760, F3Q97_01750, F3R12_04525, F9G02_11740, F9O44_07390, FE758_05775, FEM52_10640, FGZ46_12860, FJM64_15870, FQC24_10785, G0038_02490, G0040_20370, G0042_02370, G0045_07530, G0047_15245, G0048_07525, G0051_15665, G0052_07160, G0059_10130, G0061_06685, G0062_07215, G0063_17635, G0067_07710, G0069_07285, G0070_05350, G0071_14220, G0072_08335, G0074_06635, G0076_02800, G0077_07455, G0080_07285, G0084_14275, G0086_07525, G0087_07525, G0088_06635, G0089_12435, G0090_12120, G0094_10035, G0100_07525, G0101_05935, G0102_06410, G0111_05590, G0113_02570, G0117_07400, G0123_07525, G0124_07275, G0148_12300, G0157_06940, G0170_11345, G0A05_02455, G0A28_10820, G0A32_10820, G0A39_10590, G0A43_11070, G0A44_12505, G0A46_12295, G0A50_10285, G0A51_14390, G0A52_10860, G0A53_10710, G0A56_15875, G0A58_12690, G0A60_07515, G0A61_13000, G0A63_08605, G0A66_11100, G0A67_11350, G0A68_08810, G0A70_13290, G0A73_12505, G0A76_10915, G0A79_16160, G0A92_17140, G0A96_11910, G0A97_13400, G0B03_13095, G0B05_05360, G0B07_09275, G0B08_15275, G0B12_10060, G0B96_08570, G0C03_04530, G0C04_05610, G0C34_15075, G0E15_09965, G0E20_07235, G0G84_24020, G0J24_12025, G0J26_15950, G0J27_01075, G0J28_13620, G0J31_14500, G0J33_15330, G0J34_07995, G0J36_11030, G0J37_13185, G0J40_11030, G0J43_10510, G0J44_04640, G0J45_10985, G0J46_11630, G0J47_10845, G0J49_11650, G0J50_16055, G0J51_14490, G0J53_13980, G0J55_12090, G0J58_12825, G0J59_09865, G0J62_10950, G0J65_01825, G0J66_13775, G0J67_14600, G0J69_10425, G0J71_12625, G0J73_05670, G0J76_10850, G0J79_05145, G0J81_18100, G0J82_13550, G0J85_14355, G0J89_06650, G0J92_14930, G0J94_01820, G0J96_01820, G0J97_09005, G0K00_08695, G0K02_04670, G0K03_08785, G0K04_01830, G0K05_04355, G0K07_17860, G0K10_02415, G0K13_15175, G0K15_14045, G0K16_01825, G0K18_13860, G0K19_10545, G0K20_24120, G0K23_11340, G0K25_16400, G0K26_07045, G0K28_02370, G0K30_02025, G0K31_11970, G0K32_01650, G0K33_16380, G0K37_14040, G0K38_04750, G0K39_02575, G0K41_16050, G0K42_01825, G0K44_07215, G0K46_13255, G0K47_11745, G0K48_10095, G0K49_03475, G0K52_01820, G0K53_02365, G0K56_02365, G0K58_04200, G0K59_06880, G0K61_01820, G0K65_15550, G0K68_09785, G0K70_12745, G0K72_14735, G0K74_06395, G0K75_05395, G0K78_15140, G0K80_13660, G0K83_01825, G0K84_04975, G0K85_12650, G0K88_000442, G0K89_000691, G0K90_000992, G0K94_001498, G0K95_000705, G0L00_000567, G0L02_000246, G0L03_00630, G0L06_05115, G0L07_09810, G0L10_09610, G0L14_05425, G0L15_04260, G0L18_07915, G0L19_06175, G0L20_07205, G0L24_10330, G0L25_10000, G0L29_07390, G0L31_13715, G0L32_05130, G0L34_07055, G0L35_06425, G0L36_07895, G0L37_08715, G0L38_09645, G0L40_04670, G0L42_01660, G0L48_08175, G0L49_16635, G0L51_08980, G0L52_08465, G0L55_08965, G0L59_10050, G0L62_10870, G0L63_10455, G0L65_08320, G0L67_07490, G0L68_12795, G0L70_10035, G0L73_15420, G0L76_10870, G0L77_12635, G0L78_07960, G0L79_10340, G0L83_03160, G0L86_002007, G0L88_08690, G0L89_12385, G0L91_09285, G0L93_07125, G0L96_12005, G0L98_14690, G0M00_09570, G0M05_05785, G0M06_001944, G0M13_001936, G0M14_08015, G0M16_11045, G0M18_000138, G0M21_06160, G0M22_001786, G0M25_001611, G0M26_10840, G0M29_001981, G0M30_11325, G0M33_06820, G0M35_15325, G0M36_10600, G0M38_11025, G0M39_06215, G0M41_06390, G0M45_06060, G0M46_001464, G0M48_001250, G0M53_07200, G0M55_09375, G0M56_10270, G0M58_11080, G0M63_09220, G0M65_09585, G0M67_10480, G0N45_10725, G0N48_10265, G0N51_04540, G0N53_06880, G0N55_06095, G0N57_02150, G0N58_13740, G0N59_07490, G0N60_08235, G0N61_16325, G0N62_10670, G0N64_05890, G0N65_11565, G0N66_08220, G0N67_04145, G0N71_09060, G0N75_07500, G0N78_02290, G0N82_02485, G0N84_13660, G0N85_06000, G0N86_08135, G0N88_16235, G0N89_07665, G0N90_06235, G0N92_06555, G0N94_11605, G0N95_08395, G0N98_12865, G0N99_15740, G0O00_09065, G0O03_04020, G0O10_13770, G0O14_07860, G0O15_02285, G0O18_06320, G0O19_07535, G0O20_14720, G0O22_04280, G0O25_11375, G0O27_06095, G0O31_06640, G0O32_02655, G0O36_05650, G0O37_02010, G0O39_07465, G0O40_05760, G0O41_06510, G0O42_13255, G0O43_07290, G0O44_07400, G0O47_14205, G0O52_06705, G0O55_05810, G0O57_11865, G0O58_06745, G0O59_12420, G0O60_06095, G0O63_12680, G0O66_02290, G0O68_13610, G0O70_07285, G0O71_07290, G0O74_02210, G0O75_14315, G0O77_07210, G0O78_06645, G0O80_06095, G0O81_12035, G0O82_08740, G0O84_07285, G0O85_10465, G0O86_02285, G0O87_17040, G0O88_09305, G0O89_07915, G0O92_07360, G0O93_10215, G0O94_02290, G0O97_04860, G0O99_07270, G0P00_15760, G0P01_04265, G0P02_05090, G0P05_02285, G0P06_06815, G0P08_05095, G0P12_14065, G0P13_13210, G0P17_04455, G0P18_02490, G0P19_03970, G0P24_18625, G0P26_07290, G0P28_07360, G0P30_07020, G0P31_07285, G0P36_07650, G0P37_20640, G0P41_05730, G0P44_07630, G0P45_11835, G0P48_16685, G0P49_15390, G0P52_07220, G0P53_20185, G0P56_06640, G0P57_07290, G0P58_12380, G0P63_20600, G0P65_07845, G0P67_02285, G0P68_01535, G0P69_23940, G0P73_20640, G0P75_07565, G0P76_10040, G1N61_13790, G1N64_07195, G1N66_07185, G1N68_07190, G1N71_07205, G1N72_07190, G1N86_07195, G1N87_07210, G1N91_07915, G1O00_06305, G1O02_07200, G1O04_07200, G1O05_07185, G1O08_07180, G1O10_06695, G1O12_07205, G1O16_07200, G1O17_07270, G1O18_07200, G1O20_07195, G1O23_07200, G1O25_07185, G1O26_07195, G1O27_07265, G1O28_07270, G1O29_07260, G1O32_07185, G1O34_07265, G1O38_07605, G1O40_07205, G1O43_07190, G1O46_04360, G1O48_07280, G1O49_07280, G1O51_07195, G1O53_07260, G1O62_07200, G1O63_07185, G1O65_07280, G1O67_05530, G1O68_07195, G1O69_07195, G1O71_05530, G1O72_14065, G1O76_07280, G1O77_07195, G1O80_07275, G1O81_07190, G1O83_07265, G1O84_07275, G1O87_07280, G1O88_07270, G1O89_07205, G1O90_07275, G1O93_07270, G1O94_07265, G1O96_07270, G1P02_07265, G1P03_13710, G1P06_07255, G1P09_04995, G1P10_07205, G1P12_07270, G1P14_11485, G1P15_04550, G1P17_07280, G1P19_07270, G1P23_07275, G1P24_07190, G1P25_14065, G1P26_07190, G1P29_13695, G1P31_07260, G1P35_07195, G1P36_07190, G1P37_13640, G1P40_04435, G1P44_07195, G1P45_07275, G1P47_07265, G1P48_07275, G1P51_07275, G1P52_13640, G1P53_13640, G1P54_07275, G1P55_07275, G1P56_07260, G1P57_13800, G1P58_07265, G1P59_07280, G1P61_04815, G1P64_07280, G1P67_07270, G1P69_07185, G1P72_05530, G1P75_07205, G1P76_09010, G1P78_08295, G1P83_12660, G1P84_07200, G1P87_07270, G1P90_07025, G1P91_07265, G1Q03_07190, G1Q08_06365, G1Q67_07275, G1Q78_12925, G1Q81_13550, G1Q83_07275, G1Q84_06930, G1Q85_12690, G1Q86_07190, G1Q88_04360, G1Q90_07260, G1Q91_07200, G1Q93_10485, G1Q96_07165, G1Q98_07200, G1Q99_10245, G1R01_07190, G1R02_06300, G1R03_07270, G1R04_07210, G1R08_09670, G1R13_06755, G1R15_07720, G1R20_05150, G1R21_06960, G1R22_06375, G1R23_10890, G1R27_07170, G1R28_07280, G1R29_07280, G1R30_07275, G1R31_07475, G1R36_07280, G1R38_07190, G1R40_06370, G1R42_04370, G1R44_07270, G1R45_05440, G1R47_06805, G1R48_10275, G1R51_07180, G1R53_07265, G1R63_07275, G1R69_12175, G1R87_06805, G1R93_07185, G1S02_07275, G2203_14250, G2212_08285, G2218_02485, G2221_10745, G2279_02085, G2290_02370, G2793_09425, G2918_07575, G2951_04720, G3221_001889, G3230_001144, G3231_001017, G3247_003975, G3248_000573, G3254_001950, G3263_000458, G3270_001764, G3275_002227, G3312_002355, G3336_000110, G3357_002383, G3369_003947, G3433_002248, G3460_001568, G3464_003051, G3593_001456, G3A35_13615, G3V06_002985, G3V14_001335, G3V17_002289, G3V21_003223, G3V56_002025, G3V57_001521, G3X03_002826, G4189_002274, G4190_002772, G4192_002917, G4198_003122, G4201_000181, G4202_001793, G4A01_000430, G4A73_001025, G4A83_000361, G4A85_002764, G4A87_002242, G4B68_002775, G4B72_001884, G4B74_000816, G4C74_002316, G4D32_001447, G4D46_002790, G4F88_19065, G4F89_04985, G4F91_04745, G4F92_19390, G4G47_001716, G4G62_000586, G4G67_003769, G4G68_001748, G4G75_003009, G4G76_001041, G4G79_001140, G4G97_000674, G4H00_001191, G4H04_000400, G4H07_001756, G4H08_001971, G4H18_002392, G4H21_002904, G4H24_002392, G4H63_001534, G4I66_001538, G4J07_001501, G4J08_000735, G4J11_001647, G4J12_002469, G4J18_001194, G4J20_000306, G4J37_001569, G4J39_001205, G4J41_000857, G4J45_000983, G4J90_002244, G4K02_001738, G4K03_002271, G4O54_001084, G4O56_002422, G4O59_003047, G4O60_003290, G4O67_001699, G4O69_002882, G4P29_003409, G4P83_000846, G4P85_001546, G4P89_001321, G4P91_000729, G4P93_001613, G4Q12_001660, G4Q28_002044, G4Q31_002044, G4Q50_002661, G4Q52_002686, G4Q59_001483, G4Q60_002071, G4Q63_000396, G4Q67_000834, G4Q94_000749, G4R01_001476, G4R02_001772, G4R15_001499, G4R16_001783, G4W68_001733, G4W73_000989, G4W86_002100, G4W87_002333, G4W88_002237, G4W91_002441, G4Y10_002157, G9269_001679, G9302_001191, G9304_003429, G9305_000881, G9309_001414, G9313_002677, G9314_000558, G9367_002603, G9381_001460, G9C24_005004, G9C41_002881, G9C46_003677, G9C47_002671, G9C49_002994, G9C57_002493, G9C64_000447, G9G03_001977, G9G04_001540, G9G34_002737, G9G36_002821, G9G45_004809, G9G50_004881, G9G62_000377, G9W19_003070, G9W28_000397, G9W45_004733, G9W52_001879, G9W63_002850, G9W65_002051, G9W79_001697, G9W95_002052, G9W96_002121, G9X40_001725, GB021_05820, GB040_23845, GB055_12590, GB076_17280, GB106_11085, GB114_14880, GB120_16290, GB122_11945, GB131_10280, GB139_12975, GB171_11470, GB209_08765, GB221_10440, GB224_23810, GB238_09725, GB280_13060, GB321_12855, GB331_09380, GB339_05265, GB342_11210, GB368_05645, GB372_17505, GB416_07910, GB452_23275, GB459_02285, GB466_02285, GB505_13640, GB510_13415, GB551_07975, GB567_09750, GB645_08675, GBS44_07645, GBS58_02485, GBV53_05010, GBV54_09470, GBV60_06125, GBW03_05495, GBW44_06620, GBW52_11420, GBW76_07785, GBX12_13200, GBX20_07540, GBX46_05985, GBX55_04405, GBX64_11390, GBY13_02005, GBY23_09220, GBY73_07700, GBZ51_00745, GBZ55_08105, GCZ80_06970, GEZ01_15485, GJE27_08585, GJE28_12965, GNA88_000458, GNA97_000459, GNA99_000458, GNB28_000703, GNB36_002925, GNB86_002407, GNC11_002796, GNC19_002867, GNC45_003017, GNC75_002332, GNC95_002200, GT380_03950, GTH60_13330, GTH62_11235, GTH63_06790, GTH66_10405, GTH67_04550, GTH68_02490, GTH70_09105, GTH72_10285, GTH73_13410, GTH75_14215, GTH77_14130, GTH78_05095, GTH79_09985, GTH81_18200, GTH85_07220, GTH87_06095, GTH89_02175, GTH90_05500, GTH91_04745, GTH93_07285, GTH94_14500, GTH99_02170, GXC51_07385, GXC56_07385, GXG40_07385, GYI58_11515, GYI62_001473, GYI77_12910, GYJ04_04830, GYJ24_03230, GYJ27_05680, GYJ28_000393, GYJ30_07220, GYJ32_07450, GYJ53_07270, GYJ59_07685, GYJ60_07260, H8S97_14880, JJB80_14560, JJB81_14555, KP44_07635, NG06_24270, R035_04265, Z700_09655, ZV33_12495, ZX03_03825, ZY40_09830
発現宿主: Escherichia coli BL21(DE3) (大腸菌) / 参照: UniProt: A0A2J0RI82

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DNA鎖 , 2種, 2分子 EF

#3: DNA鎖 tacAT3 DNA operator


分子量: 3628.377 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)
#4: DNA鎖 tacAT3 DNA operator


分子量: 3695.443 Da / 分子数: 1 / 由来タイプ: 合成
由来: (合成) Salmonella enterica subsp. enterica serovar Typhimurium (サルモネラ菌)

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非ポリマー , 5種, 138分子

#5: 化合物 ChemComp-COA / COENZYME A / CoA


分子量: 767.534 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C21H36N7O16P3S / タイプ: SUBJECT OF INVESTIGATION
#6: 化合物 ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / (S)-2-メチル-2,4-ペンタンジオ-ル


分子量: 118.174 Da / 分子数: 3 / 由来タイプ: 合成 / 式: C6H14O2 / コメント: 沈殿剤*YM
#7: 化合物 ChemComp-BA / BARIUM ION / バリウムジカチオン


分子量: 137.327 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Ba
#8: 化合物 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / グリセロ-ル


分子量: 92.094 Da / 分子数: 2 / 由来タイプ: 天然 / 式: C3H8O3
#9: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 129 / 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

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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: 61.68 %
結晶化温度: 277 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 7
詳細: 0.08M NaCl, 0.02M BaCl, 0.04M Sodium cacodylate pH 7.0, 40% MPD, 0.012M Spermine tetrahydrochloride

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: Diamond / ビームライン: I03 / 波長: 0.97625 Å
検出器タイプ: DECTRIS EIGER2 XE 16M / 検出器: PIXEL / 日付: 2018年7月28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: 0.97625 Å / 相対比: 1
反射解像度: 1.985→86.014 Å / Num. obs: 57175 / % possible obs: 100 % / 冗長度: 12.8 % / Biso Wilson estimate: 44.16 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.163 / Rpim(I) all: 0.048 / Rrim(I) all: 0.17 / Net I/σ(I): 8.7
反射 シェル解像度: 1.985→2.02 Å / 冗長度: 12.76 % / Rmerge(I) obs: 2.654 / Num. unique obs: 2815 / CC1/2: 0.4068 / Rpim(I) all: 0.773 / Rrim(I) all: 2.767 / % possible all: 99.96

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位相決定

位相決定手法: 分子置換

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19.2_4158精密化
PHASER位相決定
PDB_EXTRACT3.27データ抽出
autoPROCデータ削減
autoPROCデータスケーリング
精密化構造決定の手法: 分子置換
開始モデル: 6G96

6g96


解像度: 2→43.39 Å / SU ML: 0.3 / 交差検証法: THROUGHOUT / σ(F): 1.36 / 位相誤差: 29.77 / 立体化学のターゲット値: ML
Rfactor反射数%反射
Rfree0.2579 2777 4.97 %
Rwork0.215 53117 -
obs0.2171 55894 99.94 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso max: 176.11 Å2 / Biso mean: 65.7658 Å2 / Biso min: 29.41 Å2
精密化ステップサイクル: final / 解像度: 2→43.39 Å
タンパク質核酸リガンド溶媒全体
原子数3926 492 134 129 4681
Biso mean--63.44 59.19 -
残基数----540
LS精密化 シェル

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20 / % reflection obs: 100 %

解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.030.36021180.371425942712
2.03-2.070.33451470.348126212768
2.07-2.110.38511370.327826342771
2.11-2.150.36441380.298326312769
2.15-2.20.34151190.278826322751
2.2-2.250.2941280.268426462774
2.25-2.310.26841280.273626532781
2.31-2.370.2981390.259226132752
2.37-2.440.2511540.245826352789
2.44-2.520.30131460.252526212767
2.52-2.610.32631290.243226542783
2.61-2.710.27521440.245826422786
2.71-2.840.26151400.229526642804
2.84-2.990.30091530.228726322785
2.99-3.170.28761520.231226632815
3.17-3.420.27171420.222126622804
3.42-3.760.21851520.194326692821
3.76-4.310.24171440.176926842828
4.31-5.430.19021280.17527292857
5.43-43.390.2541390.199928382977

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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