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

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Basic information

Entry
Database: PDB / ID: 7zg5
TitleThe crystal structure of Salmonella TacAT3-DNA complex
Components
  • (tacAT3 DNA operator) x 2
  • Acetyltransferase
  • DUF1778 domain-containing protein
KeywordsTOXIN / Toxin-antitoxin system / Salmonella / Acetyltransferase / Conditional cooperativity
Function / homology
Function and homology information


transferase activity / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Ribbon-helix-helix / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
: / COENZYME A / DNA / DNA (> 10) / Acetyltransferase / DUF1778 domain-containing protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsGrabe, G.J. / Morgan, R.M.L. / Helaine, S.
Funding support United Kingdom, European Union, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009629/1 United Kingdom
European Research Council (ERC)757369European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 United Kingdom
Wellcome Trust202926/Z/16/Z United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2024
Title: Molecular stripping underpins derepression of a toxin-antitoxin system.
Authors: Grabe, G.J. / Giorgio, R.T. / Wieczor, M. / Gollan, B. / Sargen, M. / Orozco, M. / Hare, S.A. / Helaine, S.
History
DepositionApr 1, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2Apr 3, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title
Revision 1.3Apr 10, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Acetyltransferase
B: Acetyltransferase
C: DUF1778 domain-containing protein
D: DUF1778 domain-containing protein
E: tacAT3 DNA operator
F: tacAT3 DNA operator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,54015
Polymers66,1926
Non-polymers2,3489
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16130 Å2
ΔGint-135 kcal/mol
Surface area29800 Å2
MethodPISA
Unit cell
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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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Acetyltransferase / / GNAT family N-acetyltransferase / N-acetyltransferase / Putative acetyltransferase / TacT3 toxin


Mass: 19090.840 Da / Num. of mol.: 2 / Mutation: Y143F
Source method: isolated from a genetically manipulated source
Details: Y143F
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0F7DJC6
#2: Protein DUF1778 domain-containing protein


Mass: 10343.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2J0RI82

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DNA chain , 2 types, 2 molecules EF

#3: DNA chain tacAT3 DNA operator


Mass: 3628.377 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
#4: DNA chain tacAT3 DNA operator


Mass: 3695.443 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Non-polymers , 5 types, 138 molecules

#5: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ba
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.08M NaCl, 0.02M BaCl, 0.04M Sodium cacodylate pH 7.0, 40% MPD, 0.012M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.985→86.014 Å / Num. obs: 57175 / % possible obs: 100 % / Redundancy: 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
Reflection shellResolution: 1.985→2.02 Å / Redundancy: 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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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHASERphasing
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
autoPROCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G96

6g96


Resolution: 2→43.39 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2579 2777 4.97 %
Rwork0.215 53117 -
obs0.2171 55894 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 176.11 Å2 / Biso mean: 65.7658 Å2 / Biso min: 29.41 Å2
Refinement stepCycle: final / Resolution: 2→43.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3926 492 134 129 4681
Biso mean--63.44 59.19 -
Num. residues----540
LS refinement shell

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

Resolution (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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  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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