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- PDB-7dw7: Crystal Structure of N1051A mutant of Formylglycinamidine Synthetase -

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Basic information

Entry
Database: PDB / ID: 7dw7
TitleCrystal Structure of N1051A mutant of Formylglycinamidine Synthetase
ComponentsPhosphoribosylformylglycinamidine synthase
KeywordsLIGASE / Formylglycinamide synthetase / PurL
Function / homology
Function and homology information


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / FGAR-AT PurM_N-like domain / CobB/CobQ-like glutamine amidotransferase domain / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / PurM-like, C-terminal domain ...Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / FGAR-AT PurM_N-like domain / CobB/CobQ-like glutamine amidotransferase domain / CobB/CobQ-like glutamine amidotransferase domain / Phosphoribosylformylglycinamidine synthase, linker domain / Formylglycinamide ribonucleotide amidotransferase linker domain / Phosphoribosylformylglycinamidine synthase subunit PurS-like superfamily / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSharma, N. / Tanwar, A.S. / Anand, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)DST/INT/SOUTH AFRICA/P-04/2014 India
CitationJournal: Acs Catalysis / Year: 2022
Title: Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase.
Authors: Sharma, N. / Singh, S. / Tanwar, A.S. / Mondal, J. / Anand, R.
History
DepositionJan 15, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,49064
Polymers142,4811
Non-polymers6,00963
Water21,6721203
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.626, 146.626, 141.022
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoribosylformylglycinamidine synthase / FGAMS / Formylglycinamide ribonucleotide amidotransferase / FGAR-AT


Mass: 142481.359 Da / Num. of mol.: 1 / Mutation: N1051A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: purL, purG, purI, SBOV26371, A2O69_17590, A3104_16255, A3111_08100, A3122_18440, A3146_22385, A3R41_17625, A3S30_13250, A3T21_10505, A3T81_16595, A3U32_08475, A3V03_16720, A3V89_16515, A3W57_ ...Gene: purL, purG, purI, SBOV26371, A2O69_17590, A3104_16255, A3111_08100, A3122_18440, A3146_22385, A3R41_17625, A3S30_13250, A3T21_10505, A3T81_16595, A3U32_08475, A3V03_16720, A3V89_16515, A3W57_16230, A3W75_20755, A3W86_18500, A3X15_15670, A3X55_14035, A3Y76_05480, A3Z96_12825, A4J27_15875, A4N07_15655, A4O05_06975, A4O41_14450, A4R48_16020, A6D61_24255, A9C21_04580, A9T39_19375, A9U46_14690, A9U64_15215, A9U69_19055, AAA76_16570, AAB27_11330, AAB39_12415, AAC08_06585, AAC35_16200, AAC42_09705, AAC44_12025, AAC95_16560, AAC98_09945, AAP89_12795, AAQ24_07270, AB424_15930, ABO94_11255, ABP11_16550, ABP87_05665, ABQ69_09980, ADQ28_03390, ADQ45_16805, AE787_16995, AF480_17925, AF488_17545, AF489_22720, AF497_12625, AGC55_16995, AGM99_18200, AGQ32_23665, AHN93_16575, AIC76_18365, AKH62_12480, AKH68_16995, AKI16_18240, APP08_23575, APY91_18855, AQ530_23875, AS118_03895, AT354_18810, AU613_11785, AU805_16475, AU830_15095, AU839_06730, AU951_18320, AU965_11910, AVA38_20870, AVB77_16640, AVB94_15795, AVC05_06750, AVC09_10410, AVD08_16510, AVD75_14010, AVD94_20515, AVG17_14605, AVL02_16280, AVL16_17615, AVM19_18735, AWT30_17030, AXM10_19555, AXM23_16430, AXR84_14985, AXU58_19905, AXX99_12450, B1265_16065, B1398_09135, B1642_18315, B1B86_19260, B1B89_17620, B1I91_12415, B1P38_17380, B1Q82_11795, B2E31_23025, B4V59_22480, B4W90_16890, B5A40_18360, B6362_16405, B6G98_15375, B6M25_19030, B6M43_17840, B7071_16295, B7890_22540, B7J30_12935, B7Q27_17855, B8Y16_17215, B8Y36_15580, B8Z46_18075, B9653_12045, B9C61_15035, B9C90_12665, B9C91_18265, B9C96_16400, B9M14_15595, B9O84_21470, B9U29_19195, BBQ66_17520, BEL47_16170, BGP52_19030, BIC00_17045, BIC01_21680, BIC03_14975, BIC13_15755, BK110_19395, BKM50_19320, BLB03_17550, BMG85_17290, BMS46_22775, BMU56_15580, BSC80_19775, BSD55_20250, BZ210_16255, BZG47_23445, BZN20_18305, BZZ88_07515, C4E88_18085, C5U54_19795, C5W43_24185, CA117_20565, CB102_10010, CB161_13345, CB198_03930, CB380_20190, CB383_17555, CB416_16065, CB530_14865, CB570_16700, CB657_14195, CBH20_18495, CBM40_19115, CBM67_16805, CBM76_15200, CBN77_13885, CBO42_16770, CBR08_14850, CBU32_18440, CBZ90_15660, CC339_07915, CC403_09750, CC453_10200, CC594_05605, CC725_15135, CC886_22240, CC918_14765, CC944_11990, CC971_14385, CCF93_17950, CCP17_15995, CCW27_15290, CD48_18635, CD977_22430, CDJ75_17175, CDQ60_19245, CDT37_15180, CDZ72_05835, CE355_18340, CE615_21850, CE70_16235, CE806_13055, CE87_17250, CE896_15210, CEC46_16085, CEC56_16535, CED07_14385, CEQ70_20455, CER78_17685, CET98_19110, CEY64_22365, CFB16_18015, CFB28_23180, CFE76_17880, CFE79_20830, CFF58_22075, CFF59_18880, CFJ48_18365, CGG73_23390, CHN22_16310, CI444_19665, CIX60_17685, CJC42_21375, CPR79_10095, CPS79_05985, CPX68_12615, CQE35_19945, CQG18_10955, CQO33_17440, CR370_21095, CRB02_18825, CSG22_24365, CVR97_20395, D3147_13305, D3174_00215, D3F31_09610, D3T68_00215, D3Y48_16720, D4361_16195, D4369_16945, D4380_16750, D4387_12680, D4422_14070, D4E62_19290, D4E68_15700, D4E74_19230, D4X64_15550, D4X79_12920, D4Y62_15155, D5B48_15160, D5C67_17315, D5C71_22405, D5N86_16030, D5N95_16325, D5O82_17300, D5P17_17865, D5X47_16715, D5Y28_19380, D6360_16405, D6367_17265, D6371_16345, D6373_22570, D6395_11705, D6421_22605, D6422_16430, D6J79_18305, D6K10_17770, D6P67_13400, D6Q64_21125, D6S43_16890, D6T00_15860, D6T40_17645, D7F20_16615, D7H43_17315, D7N92_13955, D7O44_22815, D8Q90_17775, D8S24_17865, D8W49_04685, D9O84_21005, DD95_10355, DJ388_18875, DJ702_22460, DK061_12960, DK631_18935, DK641_17945, DK642_10080, DK696_12090, DK698_13835, DKJ10_17715, DKR95_18750, DKS55_12840, DKU45_22760, DKU57_15990, DKU80_15995, DLB14_15700, DLB57_14330, DLB93_18200, DLR28_17285, DM322_04295, DMI89_21350, DMO92_16580, DMV40_15670, DMZ93_06125, DN165_15860, DN204_22790, DN359_20260, DNB97_23660, DNL62_16070, DNM27_16110, DNM63_13000, DNU59_13690, DNV08_16715, DNV12_14075, DNV30_16170, DNY92_11520, DNZ37_16820, DO350_18375, DO533_21640, DO585_16520, DO640_15275, DO698_10865, DO828_21380, DO960_10500, DOC60_16595, DOH72_16180, DOI32_14020, DOI53_16615, DOI92_14625, DOJ91_18820, DOQ54_15255, DOR12_17610, DOV43_10980, DOW25_17835, DP680_16650, DPB45_15245, DPB48_16730, DPD91_10520, DPD95_18900, DPF41_23405, DPF68_12070, DPK32_15240, DPL02_16870, DPP94_22595, DPP97_17500, DPS76_15800, DPT18_17685, DPU20_15725, DPY58_12185, DQ848_14480, DQ947_17390, DQ951_15690, DQC39_22590, DQC52_17305, DQD03_12855, DQD22_16910, DQE64_16525, DQK42_18425, DQQ98_13840, DQR10_14065, DQR44_14895, DQR61_12035, DQS14_13865, DQY10_15940, DQZ46_13200, DQZ56_19790, DR982_09385, DRL45_16095, DRM14_16020, DRM16_17910, DRR75_18130, DRT38_15885, DRT61_05315, DRT65_21530, DRV05_15600, DRW84_15215, DRX66_14380, DS270_13885, DS296_07805, DS451_12890, DS453_15970, DS521_15840, DS619_15480, DSF69_22175, DSG41_12910, DSM38_15480, DSN15_14920, DSR36_14390, DTE73_15610, DTF68_15005, DTG22_22705, DTG27_17970, DTW13_23245, DTW14_22955, DTW26_16940, DU223_15055, DU657_22005, DU821_16535, DU879_15365, DU924_17705, DUQ28_16005, DUQ56_15100, DUQ92_16380, DUR36_15970, DUW10_21475, DUW48_14350, DVF14_12155, DVF88_12770, DVG01_17470, DVZ53_14695, DWU22_12665, DY580_08165, DYM27_04335, DYS82_09835, DZG11_13480, E0584_18030, E0595_22890, E0935_17655, E0989_17815, E0M34_12385, E0U75_17105, E0V94_14440, E1336_04465, E1A11_17470, E5196_14165, E6W45_13110, EBB93_14240, EBC01_15760, EBD14_12425, EBD99_16685, EBK21_17215, EBO41_14340, EBP31_15665, EC404_21070, EC52_23920, ECA50_13625, ECC89_16040, ED424_14225, ED467_23130, EDL18_17295, EEK73_22610, EEQ30_09285, EER35_13770, EGL32_13655, EGN81_13750, EGU67_22080, EHB09_12375, EHB24_14185, EHB55_15660, EHC98_16430, EIE48_15360, EIW53_12810, EJI18_17070, EJO08_22055, EJO98_11125, EK393_22360, EKA25_10550, EL822_14930, ELO47_17135, ELR28_12385, ELS01_18800, EM832_22405, EM840_18120, EMN66_21115, EMY79_13250, EO190_15105, EP115_15065, EP446_07850, EPB17_11595, EPB30_16500, EPH81_14945, EPL41_15820, EQG93_18380, EQG94_22060, ERM04_17445, EU306_12095, EU349_21760, EU873_15995, EUB95_18625, EUQ56_15750, EUQ65_15405, EUQ74_17320, EUS13_13150, EVT69_16345, EVY71_12400, EW905_12415, EWB18_07440, EWE52_15635, EWJ47_14090, EWY56_21975, EWZ09_16670, EXA47_15475, EXB31_06960, EXB41_15385, EYA29_07155, EYJ91_14890, F0D96_18010, F2O93_22355, F2P00_18255, F3Q46_13285, F3Q58_12280, F3Q59_12625, F3Q65_17415, F3Q88_14500, F3Q97_13565, F3R12_19295, F3R61_12290, F3R63_16560, F9G02_13190, F9O44_17010, FE758_11065, FEM52_16235, FGZ46_15545, FJM64_20440, FL833_15175, FQC24_17960, FQD13_02595, G0038_15115, G0040_12400, G0042_16345, G0045_17160, G0047_19480, G0048_16760, G0051_18415, G0052_19200, G0059_18180, G0061_17290, G0062_17485, G0063_19430, G0067_17230, G0069_17335, G0070_13595, G0071_18860, G0072_15960, G0074_18230, G0076_17885, G0077_16555, G0080_17465, G0084_07545, G0086_18375, G0087_19350, G0088_14605, G0089_18135, G0090_17665, G0094_15775, G0100_16775, G0101_15410, G0102_17060, G0111_14900, G0113_17420, G0117_19070, G0123_17970, G0124_16720, G0148_19110, G0157_18770, G0170_07340, G0A05_16465, G0A28_11930, G0A32_14655, G0A39_22770, G0A43_21930, G0A44_16155, G0A46_13065, G0A50_15020, G0A51_15920, G0A52_11715, G0A53_14615, G0A58_14270, G0A60_14770, G0A61_14385, G0A63_12015, G0A66_15610, G0A67_14055, G0A68_13810, G0A70_14870, G0A73_15620, G0A76_09755, G0A79_16470, G0A92_13220, G0A96_21590, G0A97_13905, G0B03_18440, G0B05_17330, G0B07_17710, G0B08_16145, G0B12_16710, G0B96_18320, G0C03_16000, G0C04_14465, G0C34_19365, G0E15_17085, G0E20_23115, G0G84_12840, G0J24_18835, G0J26_17280, G0J28_17105, G0J31_11075, G0J33_15640, G0J34_17920, G0J36_18620, G0J37_17300, G0J40_18855, G0J44_14580, G0J45_18270, G0J46_16285, G0J47_18160, G0J49_19015, G0J50_16400, G0J51_18505, G0J53_18545, G0J55_13860, G0J58_19110, G0J59_16640, G0J62_18870, G0J65_17450, G0J66_15080, G0J67_18620, G0J69_18435, G0J71_15895, G0J73_17645, G0J76_16920, G0J79_20725, G0J81_17400, G0J82_17740, G0J85_19270, G0J89_16830, G0J92_15270, G0J94_17770, G0J96_16740, G0J97_18395, G0K00_18910, G0K02_17260, G0K03_19335, G0K04_18515, G0K05_07630, G0K07_13635, G0K10_15395, G0K13_19205, G0K15_19065, G0K16_17465, G0K18_15045, G0K19_12490, G0K20_16250, G0K23_18780, G0K25_17210, G0K26_16900, G0K28_17760, G0K30_15890, G0K31_15715, G0K32_07475, G0K33_16740, G0K37_16475, G0K38_17675, G0K39_07240, G0K41_02755, G0K42_16890, G0K44_17265, G0K46_18770, G0K47_19235, G0K48_16895, G0K49_16750, G0K52_17785, G0K53_17365, G0K56_17490, G0K58_13430, G0K59_17295, G0K61_17110, G0K65_18115, G0K68_14745, G0K70_17310, G0K72_18920, G0K74_19715, G0K75_18780, G0K78_20100, G0K80_15265, G0K83_15030, G0K84_16725, G0K85_17155, G0K88_002410, G0K89_002750, G0K94_000866, G0K95_002704, G0L00_002049, G0L02_002699, G0L03_03710, G0L06_04425, G0L07_07915, G0L14_09195, G0L15_13775, G0L18_16930, G0L19_16810, G0L20_08460, G0L24_11945, G0L25_11370, G0L31_08795, G0L32_17400, G0L34_09080, G0L35_05745, G0L36_14030, G0L37_15120, G0L38_12605, G0L40_09775, G0L42_08120, G0L48_03760, G0L49_20335, G0L51_13300, G0L52_09870, G0L55_13285, G0L59_13160, G0L62_13880, G0L63_13565, G0L65_12970, G0L67_14030, G0L68_13055, G0L73_15730, G0L76_08610, G0L77_13655, G0L78_12750, G0L83_05100, G0L86_002620, G0L88_12715, G0L89_13845, G0L91_13840, G0L93_11550, G0L96_13425, G0L98_10605, G0M00_10405, G0M05_08710, G0M06_002554, G0M13_002678, G0M14_11305, G0M16_10365, G0M18_001877, G0M21_07875, G0M22_002559, G0M25_002592, G0M26_14430, G0M29_002722, G0M30_12645, G0M33_11540, G0M35_15585, G0M36_08920, G0M38_12490, G0M39_17210, G0M41_18600, G0M45_16895, G0M46_002790, G0M48_003059, G0M53_13215, G0M55_12170, G0M56_14050, G0M58_14130, G0M63_13725, G0M65_13720, G0M67_13415, G0N45_17975, G0N48_18610, G0N51_21545, G0N53_19010, G0N55_16380, G0N57_11960, G0N58_14060, G0N59_04885, G0N60_19090, G0N61_18185, G0N62_16010, G0N64_17930, G0N65_18435, G0N66_17975, G0N67_18340, G0N71_23100, G0N75_04890, G0N78_16895, G0N82_17815, G0N84_18090, G0N85_18645, G0N86_18585, G0N88_18565, G0N89_19375, G0N90_17495, G0N92_17145, G0N94_12370, G0N95_17695, G0N98_14355, G0N99_12620, G0O00_14000, G0O03_18145, G0O10_18625, G0O14_09170, G0O15_17400, G0O18_18565, G0O19_17545, G0O20_17805, G0O22_18820, G0O25_15355, G0O27_16940, G0O31_17125, G0O32_16465, G0O36_03625, G0O39_18590, G0O40_18980, G0O41_18415, G0O43_19180, G0O44_18025, G0O47_18910, G0O52_16460, G0O55_18825, G0O57_17715, G0O58_16835, G0O59_22135, G0O60_19090, G0O63_18830, G0O66_17500, G0O68_18245, G0O70_18950, G0O71_17060, G0O74_19700, G0O75_17430, G0O77_19250, G0O78_17870, G0O80_18170, G0O81_16720, G0O82_16070, G0O84_19290, G0O85_19245, G0O86_17165, G0O87_19145, G0O88_22050, G0O89_19435, G0O92_19005, G0O93_13290, G0O94_17245, G0O97_08005, G0O99_12190, G0P00_22650, G0P01_12420, G0P02_19120, G0P05_16780, G0P06_18140, G0P08_19190, G0P12_22010, G0P13_18520, G0P17_16970, G0P18_18390, G0P19_18430, G0P24_12175, G0P26_16375, G0P28_16010, G0P30_19105, G0P31_19160, G0P36_14320, G0P37_14405, G0P41_11950, G0P44_13185, G0P45_16345, G0P48_19740, G0P49_03400, G0P52_19275, G0P53_08745, G0P56_18545, G0P57_18920, G0P58_07590, G0P63_11380, G0P65_17520, G0P67_15570, G0P68_05695, G0P69_12070, G0P73_23185, G0P75_09490, G0P76_16675, G1N61_16970, G1N64_17610, G1N66_17605, G1N68_17300, G1N71_17600, G1N72_17605, G1N86_17885, G1N87_17630, G1N91_17890, G1O00_17895, G1O02_17895, G1O04_17610, G1O05_17615, G1O08_14960, G1O10_16985, G1O12_17900, G1O16_17895, G1O17_17380, G1O18_17900, G1O20_17890, G1O23_16930, G1O25_17885, G1O26_17890, G1O27_16970, G1O28_17650, G1O29_16950, G1O32_17880, G1O34_17960, G1O38_17580, G1O40_17175, G1O43_17890, G1O46_17590, G1O48_17665, G1O49_17740, G1O51_17885, G1O53_17955, G1O62_17895, G1O63_17875, G1O65_16945, G1O67_17210, G1O68_17175, G1O69_17450, G1O71_17455, G1O72_17245, G1O76_17970, G1O77_17885, G1O80_17980, G1O81_17615, G1O83_17970, G1O84_17980, G1O87_17975, G1O88_17250, G1O89_17895, G1O90_17915, G1O93_17965, G1O94_17960, G1O96_17965, G1P02_17955, G1P03_18755, G1P06_16915, G1P09_17845, G1P10_17910, G1P12_17975, G1P14_15635, G1P15_19150, G1P17_17975, G1P19_17965, G1P23_17970, G1P24_17165, G1P25_15050, G1P26_17165, G1P29_18740, G1P31_17955, G1P35_17890, G1P36_17890, G1P37_18015, G1P40_17240, G1P44_17840, G1P45_17970, G1P47_17685, G1P48_19430, G1P51_17970, G1P52_18685, G1P53_19390, G1P54_17980, G1P55_17155, G1P56_17945, G1P57_17695, G1P58_17960, G1P59_17970, G1P64_17660, G1P67_17240, G1P69_17880, G1P72_14400, G1P75_17215, G1P76_17555, G1P78_13820, G1P83_13580, G1P84_17905, G1P87_17965, G1P90_17045, G1P91_17970, G1Q03_17525, G1Q08_17075, G1Q67_17970, G1Q78_16010, G1Q81_17450, G1Q83_18390, G1Q84_14285, G1Q85_17105, G1Q86_17085, G1Q88_16150, G1Q90_16655, G1Q91_16900, G1Q93_15495, G1Q96_16875, G1Q98_18110, G1Q99_12625, G1R01_18815, G1R02_17895, G1R03_17250, G1R04_17905, G1R08_15675, G1R13_16405, G1R15_15300, G1R20_17965, G1R21_16685, G1R22_17645, G1R23_15440, G1R27_17165, G1R28_17410, G1R29_17935, G1R30_17680, G1R31_17455, G1R36_18900, G1R38_16355, G1R40_17505, G1R42_17435, G1R44_17875, G1R45_15585, G1R47_17190, G1R48_15145, G1R51_17600, G1R53_18915, G1R63_17250, G1R69_15265, G1R87_18105, G1R93_17570, G1S02_17685, G2203_19045, G2212_23015, G2221_20715, G2290_18240, G2793_05005, G2918_17360, G2951_12730, G3221_002539, G3230_004711, G3231_003399, G3247_001153, G3248_002318, G3263_003677, G3270_002665, G3275_003000, G3312_003677, G3336_002551, G3357_004077, G3369_002193, G3433_004016, G3460_003578, G3464_002237, G3593_003287, G3A35_12475, G3V06_003047, G3V14_004572, G3V17_003219, G3V21_002487, G3V56_002951, G3V57_002465, G3X03_002888, G4189_002987, G4190_002834, G4192_003070, G4198_003184, G4201_004064, G4202_003684, G4A01_001873, G4A83_001144, G4A85_003523, G4A87_003005, G4B68_001939, G4B72_004037, G4B74_003265, G4C74_002568, G4D32_003975, G4D46_004522, G4F88_17560, G4F89_06480, G4F91_06140, G4F92_17885, G4G47_003503, G4G67_004065, G4G76_004374, G4G79_003639, G4G97_002925, G4H00_003595, G4H04_001581, G4H07_002134, G4H18_002025, G4H21_003081, G4H24_003251, G4H63_003364, G4I66_004155, G4J07_001295, G4J08_002243, G4J11_004388, G4J12_003047, G4J18_003345, G4J20_003779, G4J37_003529, G4J39_002444, G4J41_002216, G4J45_002224, G4J90_003426, G4K02_002931, G4K03_002599, G4O54_003128, G4O56_004528, G4O59_003109, G4O60_003053, G4O67_002513, G4O69_003565, G4P29_000798, G4P83_003070, G4P85_003673, G4P89_002793, G4P91_002816, G4P93_002597, G4Q12_003014, G4Q28_003001, G4Q31_002849, G4Q50_004508, G4Q52_004513, G4Q59_004218, G4Q60_003511, G4Q63_003524, G4Q67_001888, G4Q94_002311, G4R01_003619, G4R02_003357, G4R15_002505, G4R16_003357, G4W68_002673, G4W73_002483, G4W86_002772, G4W87_002949, G4W88_002865, G4W91_002511, G4Y10_003876, G9269_003467, G9302_003673, G9304_000307, G9305_002340, G9309_002355, G9313_003565, G9314_002114, G9367_002807, G9381_003315, G9C24_003936, G9C41_003034, G9C46_002657, G9C47_002824, G9C49_003056, G9C57_003121, G9C64_003392, G9G03_003115, G9G04_004436, G9G34_001299, G9G36_002242, G9G45_004187, G9G50_003971, G9G62_004015, G9W19_003595, G9W28_003278, G9W45_001759, G9W52_004053, G9W63_001109, G9W65_002860, G9W79_002993, G9W95_002500, G9W96_002284, G9X40_002807, GB021_20110, GB040_16750, GB076_19145, GB106_16720, GB114_16180, GB120_17000, GB122_17625, GB139_16595, GB171_15860, GB209_18280, GB221_13340, GB238_22725, GB280_17250, GB321_17045, GB339_22590, GB342_15250, GB368_17555, GB372_06965, GB416_12485, GB466_17340, GB505_16710, GB551_18050, GB645_12160, GBS58_16595, GBV60_15725, GBW03_10105, GBW44_23190, GBW52_16705, GBW76_17665, GBX20_22555, GBX55_19675, GBX64_15000, GBY13_19075, GBY23_22360, GBY73_14720, GBZ51_13310, GBZ55_11915, GCH31_16560, GCQ81_13150, GCZ80_19785, GEZ01_16345, GJE27_14165, GJE28_16750, GNA88_003122, GNA97_003638, GNA99_003153, GNB28_001815, GNB36_003103, GNC11_002490, GNC19_002264, GNC45_002507, GNC75_004447, GNC95_003325, GT380_11610, GTH60_11150, GTH62_08275, GTH63_18120, GTH66_18355, GTH67_14680, GTH68_20185, GTH70_12185, GTH72_06540, GTH73_18325, GTH75_18055, GTH77_11480, GTH78_18600, GTH79_14125, GTH81_13165, GTH85_19560, GTH87_17070, GTH89_14100, GTH90_17205, GTH91_08565, GTH93_13715, GTH94_16375, GTH99_13285, GW08_19075, GXC51_18910, GXC56_18820, GXG40_18645, GYI58_12415, GYI62_003216, GYI77_17315, GYJ04_22330, GYJ24_11935, GYJ27_22795, GYJ28_003850, GYJ30_17030, GYJ32_19920, GYJ53_17975, GYJ59_14090, GYJ60_17230, JO10_19640, KP44_18705, LZ63_24355, NG02_08255, NG06_08915, NG18_12260, NU83_23750, QA89_22595, QD15_16490, R035_16120, RJ78_17460, SAMEA4398682_01330, SE14_02783, Y934_16920, YG50_22985, YR17_11195, Z700_14825, ZB89_15590, ZC54_12160, ZT09_13285, ZT28_16520, ZT74_14230, ZT89_14865, ZU86_13885, ZU92_14585, ZV06_09880, ZV33_13900, ZV34_12770, ZV38_18010, ZV58_08705, ZV70_14590, ZV78_14095, ZW74_12645, ZX03_12360, ZX26_16475, ZY23_15400, ZY27_16350, ZY40_07130, ZY51_04455, ZZ18_14120, ZZ43_10415, ZZ77_11510, ZZ79_09255
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6F9Y3, phosphoribosylformylglycinamidine synthase

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Non-polymers , 5 types, 1266 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 3.1 Å3/Da / Density % sol: 60.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.587 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.587 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 158641 / % possible obs: 100 % / Redundancy: 8 % / Rpim(I) all: 0.023 / Net I/σ(I): 34.5
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 7938 / CC1/2: 0.931

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T3T

1t3t


Resolution: 1.8→47.99 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.641 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1625 8052 5.1 %RANDOM
Rwork0.133 ---
obs0.1345 150265 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.79 Å2 / Biso mean: 22.178 Å2 / Biso min: 9.83 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.8→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9927 0 371 1203 11501
Biso mean--46.53 29.83 -
Num. residues----1290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.01910680
X-RAY DIFFRACTIONr_bond_other_d0.0030.0210112
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.97914485
X-RAY DIFFRACTIONr_angle_other_deg1.181323253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.97651357
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.11324.016498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.95151707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9531582
X-RAY DIFFRACTIONr_chiral_restr0.1450.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02112093
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022440
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 568 -
Rwork0.194 11080 -
all-11648 -
obs--99.88 %

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