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- PDB-7ak7: Structure of Salmonella TacT2 toxin bound to TacA2 antitoxin -

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Basic information

Entry
Database: PDB / ID: 7ak7
TitleStructure of Salmonella TacT2 toxin bound to TacA2 antitoxin
Components
  • Acetyltransferase
  • CopG family transcriptional regulator
KeywordsTOXIN / Acetyltransferase / antitoxin / GNAT / Salmonella
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Protein of unknown function (DUF1778) / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
ACETYL COENZYME *A / Acetyltransferase / CopG family transcriptional regulator
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsGrabe, G.J. / Morgan, R.M.L. / Hare, S.A. / Helaine, S.
Funding support United Kingdom, 4items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/M009629/1 United Kingdom
European Research Council (ERC)757369 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/D524840/1 United Kingdom
Wellcome Trust202926/Z/16/Z United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2021
Title: Auxiliary interfaces support the evolution of specific toxin-antitoxin pairing.
Authors: Grabe, G.J. / Giorgio, R.T. / Hall, A.M.J. / Morgan, R.M.L. / Dubois, L. / Sisley, T.A. / Rycroft, J.A. / Hare, S.A. / Helaine, S.
History
DepositionSep 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_contact_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 1, 2021Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Acetyltransferase
B: Acetyltransferase
C: CopG family transcriptional regulator
D: CopG family transcriptional regulator
E: CopG family transcriptional regulator
F: CopG family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0539
Polymers80,3996
Non-polymers1,6553
Water5,783321
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.491, 54.452, 76.900
Angle α, β, γ (deg.)100.570, 97.730, 117.000
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17923.770 Da / Num. of mol.: 2 / Mutation: Y137F, E29K
Source method: isolated from a genetically manipulated source
Details: N-terminal GS is a vector remnant. / Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: A3104_12120, A3S30_09335, A3T81_08410, A3U32_18895, A3V03_06630, A3V89_04715, A3W57_09370, A3W75_08380, A3X15_08985, A3X55_16410, A3Y76_14810, A4N07_10055, A4O05_19285, A4O41_13420, A4R48_ ...Gene: A3104_12120, A3S30_09335, A3T81_08410, A3U32_18895, A3V03_06630, A3V89_04715, A3W57_09370, A3W75_08380, A3X15_08985, A3X55_16410, A3Y76_14810, A4N07_10055, A4O05_19285, A4O41_13420, A4R48_14945, A6D61_23370, AAA76_04890, AAB27_06080, AAB79_07335, AAC35_12485, ADQ28_16395, AF497_17060, AGM99_01705, AHN93_01715, AKH62_11990, AL144_08340, AL168_06480, AL184_07135, AQ530_03720, AU613_02445, AVA38_05020, AVC05_08125, AVL16_17225, AWT30_10165, AXX99_06220, B1265_01705, B1398_23245, B1642_15800, B1P38_05125, B2E31_22085, B4V59_04040, B4W90_15110, B6362_05795, B7Q27_01705, B8Y16_22745, B8Z46_15755, B9C90_11205, B9C96_14245, B9M14_07745, B9O84_03860, BBQ66_22395, BIC00_15285, BIC13_14710, BK110_14120, BKM50_18920, BMS46_01705, BMU56_14770, BZ203_07155, BZZ88_08270, C5W43_08435, CA117_06825, CB102_09090, CB198_03545, CB570_03095, CB646_12985, CBM67_08535, CBM76_05080, CBZ90_21895, CC339_11425, CC403_11745, CC453_16245, CC652_15015, CC971_08570, CCP17_01700, CDZ72_15910, CE70_13730, CED07_02455, CEQ70_07710, CFF58_07755, CFF59_21595, CHN22_20110, CIX60_06815, CPS79_04970, CQO33_23140, CSG22_03750, CVR97_08925, D4361_13195, D4387_09195, D4422_08350, D5823_02245, D5N86_13565, D5N95_11060, D5O82_11205, D5P17_16870, D5X47_12830, D5Y28_14825, D6422_03935, D6J79_15995, D8S24_15270, DD95_21775, DLB93_15585, DLR28_22745, DMI89_21300, DMO92_15470, DN165_12420, DNB97_07960, DNM27_06425, DNZ37_16415, DO533_20150, DP680_12765, DPB42_04130, DPD91_13885, DPF41_22710, DPF68_06925, DPS76_13305, DQD22_13230, DQR44_14440, DRM14_09995, DRR75_21965, DRT38_11500, DRT61_02580, DRV05_13390, DSF94_15305, DTF68_14145, DU071_20475, DU657_04175, DU879_07275, DWU22_16770, DY580_18910, DYM27_17255, E0935_09170, E1A11_12005, E6W45_15420, EBD14_13825, EBK21_16640, EC404_21665, EEQ30_21810, EER35_15280, EHB09_19970, EL822_14495, ELS01_18365, EPB30_15210, EQG93_09755, EVY71_07905, F0D96_14080, F2P00_16195, F3Q97_09870, F3R12_05240, F9G02_11145, F9O44_17810, FEM52_15650, FGZ46_10925, FQC24_13060, G0038_10890, G0040_04675, G0042_08320, G0045_13120, G0047_14485, G0048_13540, G0051_12080, G0052_16430, G0059_11660, G0061_12550, G0062_13130, G0063_16480, G0067_14185, G0069_13405, G0070_09580, G0071_13165, G0072_10940, G0074_13530, G0076_16085, G0077_13470, G0080_15595, G0084_16165, G0086_14475, G0087_13540, G0088_12550, G0089_06955, G0090_15400, G0094_13455, G0100_13300, G0101_10015, G0102_12635, G0111_18015, G0113_14145, G0117_15065, G0123_13540, G0124_10550, G0148_10680, G0157_12960, G0170_15225, G0A05_04970, G0A32_22495, G0A39_21715, G0A43_21070, G0A44_10190, G0A46_23355, G0A50_09160, G0A51_09465, G0A52_05930, G0A53_08765, G0A58_08665, G0A60_22620, G0A61_13425, G0A63_05005, G0A66_09670, G0A67_23690, G0A68_05880, G0A70_09080, G0A73_10190, G0A76_21905, G0A79_05455, G0A92_11430, G0A96_13675, G0A97_21725, G0B03_22870, G0B05_23635, G0B07_23665, G0B08_05105, G0B12_23035, G0B96_04990, G0C03_13210, G0C04_15865, G0E15_14995, G0E20_06345, G0G84_17325, G0J24_22425, G0J26_22635, G0J27_06420, G0J28_22920, G0J31_06945, G0J33_21870, G0J34_23190, G0J36_22945, G0J37_21650, G0J40_23005, G0J43_01745, G0J44_22205, G0J45_23245, G0J46_23065, G0J47_22375, G0J49_23025, G0J50_01755, G0J51_22440, G0J53_09480, G0J55_22080, G0J58_09970, G0J59_11780, G0J62_09150, G0J65_12065, G0J66_08650, G0J67_13775, G0J69_14065, G0J71_10850, G0J73_04195, G0J76_10025, G0J79_11245, G0J81_14005, G0J82_04065, G0J85_13545, G0J89_01755, G0J92_14060, G0J94_04610, G0J96_11350, G0J97_18265, G0K00_22985, G0K02_14220, G0K03_22870, G0K04_03410, G0K05_16970, G0K07_12990, G0K10_13820, G0K13_11725, G0K15_23065, G0K16_11720, G0K18_04915, G0K19_12945, G0K20_15760, G0K23_22845, G0K25_09170, G0K26_10780, G0K28_13685, G0K30_10450, G0K31_06645, G0K32_14525, G0K33_13465, G0K37_10165, G0K38_06915, G0K39_19210, G0K41_01330, G0K42_13670, G0K44_13055, G0K46_15520, G0K47_22675, G0K48_01755, G0K49_15025, G0K52_04605, G0K53_05150, G0K56_04845, G0K58_19750, G0K59_01755, G0K61_09120, G0K65_11540, G0K68_01745, G0K70_11920, G0K72_11520, G0K74_07905, G0K75_13605, G0K78_05725, G0K80_01750, G0K83_07710, G0K84_15620, G0K85_01755, G0K88_002893, G0K89_002653, G0K90_002299, G0K94_003123, G0K95_003254, G0L00_001896, G0L02_003282, G0L03_12250, G0L06_17545, G0L07_17230, G0L10_17595, G0L14_19275, G0L15_13250, G0L18_11955, G0L19_06530, G0L20_07545, G0L24_08975, G0L25_10820, G0L29_10295, G0L31_19505, G0L32_13795, G0L34_15735, G0L35_12260, G0L36_22645, G0L37_19225, G0L38_11830, G0L42_10150, G0L48_15340, G0L49_23575, G0L51_09770, G0L52_08805, G0L55_09755, G0L59_07195, G0L62_08975, G0L63_08580, G0L65_09630, G0L67_08280, G0L68_08295, G0L73_00610, G0L76_11775, G0L77_07140, G0L78_21395, G0L79_07610, G0L83_06545, G0L86_001734, G0L89_08855, G0L91_11580, G0L93_04530, G0L96_08810, G0L98_04525, G0M00_04585, G0M05_08330, G0M06_001524, G0M13_001301, G0M14_10405, G0M16_09985, G0M18_000610, G0M21_06500, G0M22_001518, G0M25_001338, G0M26_07895, G0M29_001533, G0M30_03245, G0M33_07230, G0M35_03415, G0M36_02605, G0M38_05515, G0M39_09815, G0M41_18395, G0M45_09645, G0M46_001723, G0M48_002290, G0M53_05780, G0M55_07955, G0M56_08845, G0M58_08865, G0M63_11630, G0M65_07370, G0M67_09060, G0N45_13635, G0N48_14240, G0N51_22085, G0N53_10795, G0N55_12030, G0N57_21870, G0N58_10595, G0N59_17775, G0N60_15985, G0N61_10005, G0N62_13340, G0N64_11655, G0N65_16220, G0N66_16880, G0N67_13425, G0N71_22370, G0N75_16310, G0N78_13040, G0N82_11175, G0N84_15550, G0N85_16010, G0N86_16525, G0N88_11260, G0N89_11430, G0N90_14485, G0N92_12800, G0N94_04985, G0N95_14780, G0N98_04870, G0N99_06395, G0O00_05895, G0O10_16565, G0O14_19230, G0O15_07210, G0O19_13605, G0O20_06040, G0O22_15265, G0O25_12175, G0O27_10555, G0O31_11480, G0O32_18160, G0O37_07240, G0O39_16330, G0O40_13840, G0O41_10970, G0O42_04795, G0O43_16235, G0O47_10165, G0O52_12130, G0O55_12070, G0O57_04795, G0O58_15170, G0O59_07005, G0O60_12305, G0O63_05890, G0O66_07420, G0O68_11005, G0O70_12160, G0O71_10365, G0O74_04610, G0O75_10325, G0O77_18530, G0O78_10175, G0O80_11950, G0O81_07775, G0O82_17535, G0O84_11950, G0O85_16080, G0O86_04690, G0O87_13740, G0O89_17200, G0O92_14705, G0O93_22115, G0O94_05025, G0O97_06375, G0O99_03660, G0P00_06030, G0P01_07100, G0P02_09755, G0P05_04695, G0P06_12305, G0P08_07505, G0P12_04040, G0P13_16855, G0P17_11535, G0P18_16385, G0P19_12505, G0P24_09115, G0P26_10365, G0P28_12465, G0P30_10300, G0P31_14035, G0P36_22340, G0P37_07770, G0P41_07620, G0P44_09640, G0P45_11330, G0P48_11530, G0P49_04870, G0P52_09195, G0P53_13655, G0P56_11545, G0P57_10570, G0P58_13635, G0P65_09845, G0P67_06460, G0P69_03850, G0P73_18480, G0P75_21930, G0P76_04980, G1N61_11430, G1N64_13125, G1N66_13115, G1N68_12810, G1N71_13960, G1N72_13120, G1N86_14260, G1N87_13140, G1N91_14980, G1O00_13370, G1O02_14265, G1O04_13130, G1O05_13115, G1O08_14245, G1O10_14575, G1O12_14270, G1O16_14265, G1O17_12890, G1O18_14265, G1O20_14260, G1O23_13130, G1O25_14255, G1O26_14260, G1O27_13195, G1O28_14025, G1O29_13190, G1O32_14250, G1O34_14330, G1O38_14670, G1O40_14270, G1O43_14255, G1O46_13960, G1O48_14035, G1O49_13245, G1O51_14260, G1O53_14325, G1O62_14265, G1O63_14250, G1O65_14035, G1O67_13580, G1O68_12430, G1O69_13820, G1O71_13815, G1O72_12565, G1O76_14345, G1O77_14260, G1O80_14350, G1O81_13120, G1O83_14850, G1O84_14340, G1O87_14345, G1O88_14335, G1O89_14270, G1O90_14340, G1O93_14335, G1O94_14330, G1O96_14335, G1P02_14330, G1P03_15065, G1P06_14010, G1P09_13285, G1P10_14285, G1P12_14335, G1P14_10885, G1P15_14680, G1P17_14350, G1P19_14335, G1P23_14340, G1P24_14255, G1P25_12565, G1P26_14255, G1P29_15050, G1P31_14325, G1P35_14260, G1P36_14255, G1P37_14995, G1P40_14330, G1P44_14260, G1P45_14340, G1P47_13195, G1P48_14340, G1P51_14340, G1P52_14995, G1P53_14995, G1P54_14350, G1P55_14030, G1P56_14320, G1P57_11430, G1P58_14330, G1P59_14345, G1P61_21930, G1P64_14035, G1P67_14335, G1P69_14250, G1P72_21350, G1P75_14280, G1P76_13925, G1P78_18450, G1P83_17560, G1P84_14265, G1P87_14335, G1P90_14070, G1P91_14330, G1Q03_13945, G1Q08_13430, G1Q67_14340, G1Q78_10585, G1Q81_12050, G1Q83_13210, G1Q84_25010, G1Q85_15060, G1Q86_13435, G1Q88_13240, G1Q90_12880, G1Q91_13130, G1Q93_09880, G1Q96_13095, G1Q98_12620, G1Q99_13085, G1R01_14255, G1R02_13365, G1R03_14335, G1R04_14280, G1R08_11025, G1R13_12645, G1R15_10150, G1R20_15055, G1R21_12185, G1R22_11995, G1R23_09470, G1R27_12715, G1R28_13785, G1R29_14345, G1R30_14035, G1R31_12960, G1R36_14345, G1R38_12170, G1R40_12965, G1R42_14260, G1R44_14025, G1R45_13170, G1R47_13560, G1R48_07150, G1R51_13110, G1R53_14345, G1R63_14340, G1R69_22240, G1R87_12690, G1R93_13940, G1S02_13205, G2203_17005, G2212_21725, G2218_05685, G2279_10705, G2290_05915, G2793_13260, G2918_01710, G2951_10855, G3221_002152, G3230_002352, G3231_002329, G3247_003929, G3248_002090, G3254_003042, G3263_001043, G3270_000263, G3275_002634, G3312_002755, G3336_001816, G3357_000870, G3369_004068, G3433_000550, G3460_002178, G3464_000174, G3593_002448, G3A35_04735, G3V06_001254, G3V14_001801, G3V17_002475, G3V21_004267, G3V56_002586, G3V57_002113, G3X03_000690, G4189_004414, G4190_001830, G4192_001070, G4198_000722, G4201_003838, G4202_000541, G4A01_001125, G4A73_001460, G4A83_000816, G4A85_001121, G4A87_002649, G4B68_004084, G4B72_003983, G4B74_005051, G4C74_001506, G4D46_004359, G4F88_02960, G4F89_21410, G4F91_21065, G4F92_02960, G4G47_000344, G4G62_002266, G4G67_004381, G4G68_001972, G4G75_004543, G4G76_002011, G4G79_000541, G4G97_001003, G4H00_001881, G4H04_001650, G4H07_002057, G4H08_002153, G4H18_002942, G4H21_002050, G4H24_002944, G4H63_001839, G4I66_004461, G4J07_000549, G4J08_004000, G4J11_004335, G4J12_001917, G4J18_002331, G4J20_000821, G4J37_001932, G4J39_001776, G4J41_001379, G4J45_004817, G4J90_001159, G4K02_004201, G4K03_001199, G4O54_004550, G4O56_004389, G4O59_001070, G4O60_000938, G4O67_002604, G4O69_004762, G4P29_003634, G4P83_002042, G4P85_001310, G4P89_001919, G4P91_002666, G4P93_000965, G4Q12_002354, G4Q28_002639, G4Q31_002633, G4Q50_004407, G4Q52_004412, G4Q59_003138, G4Q60_001549, G4Q63_001450, G4Q67_001703, G4Q94_001634, G4R01_003204, G4R02_000965, G4R15_004219, G4R16_002635, G4W68_002585, G4W73_001768, G4W86_002507, G4W87_002479, G4W88_001855, G4W91_002117, G4Y10_004542, G9269_001448, G9302_002108, G9304_004849, G9305_002227, G9309_002205, G9313_001478, G9314_004181, G9367_002187, G9381_001257, G9C24_000567, G9C41_001675, G9C46_001943, G9C47_000939, G9C49_001734, G9C57_002902, G9C64_001620, G9G03_004433, G9G04_002015, G9G34_000436, G9G36_001174, G9G45_002398, G9G50_000972, G9G62_001468, G9W19_000502, G9W28_000882, G9W45_004409, G9W52_003492, G9W63_003255, G9W65_002641, G9W79_002187, G9W95_002772, G9W96_002207, G9X40_003197, GB021_08610, GB040_11000, GB055_01690, GB076_04540, GB106_04370, GB114_04010, GB120_07305, GB122_01710, GB131_04450, GB139_08410, GB171_05865, GB209_14140, GB221_02680, GB224_07950, GB238_22200, GB280_15295, GB321_15090, GB331_06100, GB339_22080, GB342_09815, GB368_02670, GB372_02645, GB416_20560, GB452_10735, GB459_05025, GB466_07210, GB505_01705, GB510_08355, GB551_13470, GB567_07870, GB645_04880, GBS44_18785, GBS58_09475, GBV53_22625, GBV54_07515, GBV60_21900, GBW03_09675, GBW44_22665, GBW52_08655, GBW76_05035, GBX12_14980, GBX20_03685, GBX46_04795, GBX55_05100, GBX64_17785, GBY13_09945, GBY23_23515, GBY73_10470, GBZ51_12295, GBZ55_09045, GCZ80_05980, GEZ01_14630, GJE27_13305, GJE28_10415, GNA88_000944, GNA97_001010, GNA99_000944, GNB28_000864, GNB36_002418, GNB86_002589, GNC11_002878, GNC19_004691, GNC45_004353, GNC75_004303, GT380_09545, GTH60_14365, GTH62_12140, GTH63_11000, GTH67_08490, GTH68_14710, GTH70_12630, GTH73_09085, GTH75_09920, GTH77_07850, GTH78_07495, GTH79_03555, GTH81_10095, GTH85_10805, GTH87_13980, GTH89_09640, GTH90_12195, GTH91_11435, GTH93_15185, GTH94_11895, GTH99_08435, GXC51_01700, GXC56_01700, GXG40_01700, GYI58_05930, GYI62_004436, GYI77_08050, GYJ04_14900, GYJ27_21435, GYJ28_001326, GYJ30_12455, GYJ32_16115, GYJ53_14345, GYJ59_09845, GYJ60_14325, H8S97_22020, KP44_01705, NG06_07900, R035_20160, SE14_04559, STMLT2P22_CBEKMEGD_00474, Z700_13200, ZV33_08625, ZX03_01890, ZY40_08380
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6HSU7
#2: Protein
CopG family transcriptional regulator / DUF1778 domain-containing protein / TacA2 antitoxin


Mass: 11137.742 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: N-terminal GS is a vector remnant. / Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: STY4517, A2O69_04830, A3104_12125, A3111_16100, A3122_04225, A3146_12185, A3R41_05780, A3S30_09340, A3T21_16590, A3T81_08415, A3U32_18900, A3V03_06635, A3V89_04720, A3W57_09375, A3W75_08385, ...Gene: STY4517, A2O69_04830, A3104_12125, A3111_16100, A3122_04225, A3146_12185, A3R41_05780, A3S30_09340, A3T21_16590, A3T81_08415, A3U32_18900, A3V03_06635, A3V89_04720, A3W57_09375, A3W75_08385, A3W86_08895, A3X15_08990, A3X55_16415, A3Y76_14815, A3Z96_24840, A4J27_15475, A4N07_10060, A4O05_19290, A4O41_13425, A4R48_14940, A6D61_23375, A9C21_15195, A9S84_16305, A9T17_24610, A9T39_04435, A9U46_16020, A9U64_07345, AAA76_04895, AAB27_06085, AAB39_05200, AAB79_07340, AAC08_17465, AAC35_12490, AAC42_06110, AAC95_01705, AAC98_04620, AAP89_11820, AAQ24_02940, AB424_12745, ABO94_05745, ABP11_11060, ABP54_03380, ABQ69_19040, ADQ28_16390, ADQ45_04785, AE787_07315, AF480_07975, AF488_05300, AF489_07575, AF497_17065, AGC55_17340, AGM99_01710, AGQ32_12045, AH984_04205, AHN93_01720, AIC76_06295, AKH62_11995, AKH68_21495, AKI16_06210, AL144_08345, AL151_04855, AL154_03280, AL166_08595, AL168_06485, AL170_10390, AL174_18775, AL184_07140, APH22_16760, APP08_09505, APY91_14235, AQ530_03725, AS118_18525, AT354_15380, AU613_02440, AU805_09140, AU830_10285, AU839_09530, AU951_00620, AU965_04915, AVA38_05025, AVB77_03230, AVB94_07720, AVC05_08130, AVC09_00615, AVD75_11750, AVD94_20895, AVG17_14180, AVL02_10840, AVL16_17220, AVM19_15250, AVM22_23420, AWT30_10170, AXM10_05785, AXM23_10860, AXR84_09430, AXU58_11130, AXX99_06225, B1265_01710, B1398_23250, B1642_15805, B1B86_01710, B1B89_08315, B1I91_16585, B1P38_05130, B1Q82_03960, B2E31_22090, B4V59_04045, B4W90_15115, B5A40_15890, B6362_05800, B6G98_03955, B6M25_08550, B6M43_04700, B7071_21440, B7890_21810, B7J30_20630, B7Q27_01710, B8Y16_22750, B8Y36_13865, B8Z46_15760, B9653_06255, B9C61_11525, B9C71_12215, B9C90_11200, B9C91_15880, B9C96_14250, B9M14_07750, B9O84_03865, B9U29_16925, BBQ66_22400, BEL47_01700, BGP52_12050, BIC00_15290, BIC01_07585, BIC03_01705, BIC13_14715, BK110_14125, BKM50_18925, BLB03_06650, BMS46_01710, BMU56_14775, BSC80_10970, BSD55_23050, BZ203_07160, BZ210_05600, BZG47_12380, BZN20_21955, BZZ88_08275, C4E88_07135, C5U54_10255, C5W43_08440, CA117_06830, CB102_09095, CB161_12435, CB198_03550, CB383_17145, CB416_15020, CB570_03100, CB646_12990, CB657_13120, CBH20_16570, CBM40_09235, CBM67_08540, CBM76_05085, CBN77_16225, CBO42_07645, CBR08_06655, CBU32_08560, CBZ90_21900, CC339_11430, CC403_11750, CC453_16250, CC594_18870, CC652_15020, CC725_12230, CC886_21755, CC918_20825, CC971_08575, CCF93_09515, CCP17_01705, CCW27_10850, CD48_08120, CD977_03275, CDJ75_10025, CDT37_01705, CDZ72_15915, CE355_15790, CE615_11295, CE70_13735, CE806_06620, CE87_06570, CE896_03030, CEC46_13770, CEC56_15565, CED07_02450, CEQ70_07715, CER78_14360, CET98_15920, CEY64_08970, CFB16_04515, CFB28_08430, CFE76_15065, CFE79_07710, CFF58_07760, CFF59_21600, CFJ48_12970, CGG73_09310, CHN22_20115, CI444_09245, CIX60_06810, CJC42_18860, CPR79_08375, CPS79_04975, CPX68_11005, CQE35_09575, CQG18_10495, CQO33_23145, CR370_14620, CRB02_04225, CSG22_03755, CTJ81_14475, CVR97_08920, D3147_12900, D3174_12515, D3F31_17570, D3T68_19740, D3Y48_22090, D4361_13200, D4369_13900, D4380_15290, D4387_09200, D4422_08355, D4E62_18870, D4E68_11140, D4E74_16080, D4X64_22990, D4X79_14400, D4Y62_07960, D5823_02250, D5949_04945, D5B48_05985, D5C67_15220, D5C71_22800, D5N86_13570, D5N95_11065, D5O82_11210, D5P17_16875, D5X47_12835, D5Y28_14830, D6360_13875, D6367_01775, D6371_15020, D6373_22960, D6395_11270, D6421_22990, D6422_03940, D6J79_16000, D6K10_15800, D6P67_10040, D6S43_11565, D6T00_15005, D6T40_17210, D7F20_11850, D7H43_04840, D7N92_15415, D7O44_23205, D8S24_15275, DD95_21770, DJ388_06405, DJ702_21955, DK061_12005, DK631_22150, DK641_07990, DK642_14995, DK689_16610, DK696_10480, DK698_12575, DKJ10_03885, DKJ21_24750, DKR95_23780, DKS55_06660, DKU45_02600, DKU57_12910, DKU80_11870, DLB14_03640, DLB57_13375, DLB93_15590, DLR28_22750, DM322_08735, DMI89_21305, DMO92_15475, DMV40_10160, DMZ93_16755, DN165_12415, DN204_23180, DN359_15890, DNB97_07965, DNL62_06005, DNM27_06430, DNM63_04665, DNU59_12465, DNV08_16265, DNY92_12000, DNZ37_16420, DO350_13260, DO533_20155, DO585_14500, DO640_10995, DO698_21325, DO766_14485, DO960_10100, DOC60_13885, DOH72_08990, DOI32_07275, DOI53_16175, DOI92_01265, DOJ39_17870, DOJ91_20010, DOQ54_13620, DOQ88_14045, DOR12_12795, DOW25_08025, DP680_12770, DPB42_04135, DPB45_12875, DPB48_10435, DPB57_14405, DPD91_13890, DPD95_14660, DPD99_07790, DPF41_22715, DPF68_06930, DPK32_13610, DPK79_12210, DPL02_15330, DPP94_22985, DPS76_13310, DPU20_09230, DQ848_14045, DQ947_04090, DQ951_16680, DQC39_22985, DQC52_23140, DQD22_13225, DQE64_14105, DQE65_15845, DQK42_16030, DQR10_17820, DQR44_14445, DQS14_15905, DQY10_22630, DQZ46_12750, DQZ56_10175, DR982_12980, DRL45_09855, DRM14_10000, DRM16_13190, DRR75_21970, DRT38_11505, DRT61_02585, DRT65_12290, DRV05_13395, DRW84_10155, DRX66_11400, DS296_10255, DS453_14715, DS619_08355, DSF69_22565, DSF94_15310, DSM38_15030, DSN15_21865, DSR36_09395, DTE73_12195, DTF68_14150, DTG22_17535, DTG27_04610, DTW13_22385, DTW14_23350, DTW26_13730, DU071_20480, DU657_04180, DU821_12055, DU879_07280, DUQ28_08770, DUQ56_13065, DUQ92_07010, DUW48_13490, DVF14_14365, DVF88_13730, DVG01_02530, DVZ53_14165, DWU22_16775, DY580_18915, DYM27_17260, DYS82_07805, DZG11_07810, E0584_10585, E0595_22380, E0935_09175, E0989_14220, E0M34_08655, E0U75_14625, E0V94_12675, E1A11_12010, E1A20_04620, E5196_12370, E6W45_15425, EBC01_12685, EBD14_13830, EBK21_16645, EBL31_13785, EBO41_10395, EBP31_14040, EC404_21670, EC52_04050, ECA50_08690, ECC89_13490, ED424_13845, ED467_22615, EDL18_14745, EEK73_21530, EEQ30_21815, EER35_15285, EGN81_10220, EGU67_22475, EGU98_12825, EHB09_19975, EHB24_13180, EHC98_15145, EIE48_12945, EIW53_11885, EJI18_16640, EJO08_22445, EJO98_07025, EKA25_12110, EL822_14500, ELO47_13850, ELR28_11565, ELS01_18370, EM832_22795, EM840_14640, EMN66_15280, EMY79_10355, EO190_06835, EP446_01035, EPB30_15215, EPH81_09830, EQG93_09760, EQG94_22450, ERM04_13190, EU306_14230, EU349_22150, EUB95_22555, EUQ56_14705, EUQ65_01755, EUQ74_15275, EUS13_12180, EVY71_07900, EWB18_00620, EWE52_06800, EWJ47_13005, EWZ09_12070, EXA47_13190, EXB31_11140, EXB41_13600, EYA29_12720, EYJ91_14485, F0D96_14075, F2O93_10970, F2P00_16200, F3Q46_00300, F3Q58_05940, F3Q59_00435, F3Q88_05750, F3Q97_09865, F3R12_05235, F3R61_00300, F3R63_13825, F9G02_11140, F9O44_17815, FEM52_15655, FGZ46_10920, FQC24_13065, FQD13_16090, GCH31_09085, GCZ80_05985, GEZ01_14635, GW08_08845, JO10_09985, KP44_01710, LZ63_09660, NCTC13348_02288, NG02_17950, NG06_07905, NG18_21940, NU83_23015, QA89_21480, QB40_12820, QD15_12985, R035_20165, RJ78_05095, SAMEA4398682_04321, SE14_04558, Y934_12485, YG50_21405, YR17_04665, Z700_13205, ZB89_15140, ZC54_11150, ZT09_03135, ZT28_02460, ZT74_07710, ZT89_07650, ZU86_06785, ZU92_08685, ZV06_04225, ZV33_08630, ZV34_09010, ZV38_21720, ZV58_02460, ZV70_03190, ZV78_02855, ZV90_19040, ZW74_08020, ZX03_01895, ZY00_12875, ZY23_10425, ZY27_08590, ZY40_08385, ZY51_00615, ZZ18_04390, ZZ43_06690, ZZ77_04740, ZZ79_20260
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0D6HUM3
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H38N7O17P3S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01M Magnessium chloride hexahydrate 0.05M MES monohydrate 1.8M Lithium sulfate monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.14→73.22 Å / Num. obs: 36519 / % possible obs: 97.1 % / Redundancy: 1.8 % / Biso Wilson estimate: 29.113 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.073 / Rrim(I) all: 0.103 / Net I/σ(I): 3.8
Reflection shell

Diffraction-ID: 1 / Redundancy: 1.8 %

Resolution (Å)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
2.14-2.181.2310317380.5140.72692.2
5.81-73.267.1327318680.0330.04799

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data scaling
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FVJ

5fvj


Resolution: 2.14→46.66 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.907 / SU B: 8.511 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.299 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2634 1795 4.9 %RANDOM
Rwork0.2197 ---
obs0.2219 34696 97.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.27 Å2 / Biso mean: 37.95 Å2 / Biso min: 20.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å2-0.01 Å20.05 Å2
2---0.05 Å20.04 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.14→46.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 103 321 5247
Biso mean--44.5 41.47 -
Num. residues----625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0135008
X-RAY DIFFRACTIONr_bond_other_d0.0020.0174891
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.6596796
X-RAY DIFFRACTIONr_angle_other_deg1.2651.58111222
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5545619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.41620.432278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.94215860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9161555
X-RAY DIFFRACTIONr_chiral_restr0.0630.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025596
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021116
LS refinement shellResolution: 2.14→2.2 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.316 144 -
Rwork0.313 2457 -
obs--93.63 %

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