[日本語] English
万見
- PDB-7dw7: Crystal Structure of N1051A mutant of Formylglycinamidine Synthetase -

+
データを開く


IDまたはキーワード:

読み込み中...

-
基本情報

登録情報
データベース: PDB / ID: 7dw7
タイトルCrystal Structure of N1051A mutant of Formylglycinamidine Synthetase
要素Phosphoribosylformylglycinamidine synthase
キーワードLIGASE / Formylglycinamide synthetase / PurL
機能・相同性
機能・相同性情報


phosphoribosylformylglycinamidine synthase / phosphoribosylformylglycinamidine synthase activity / 'de novo' IMP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / cytoplasm
類似検索 - 分子機能
Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / 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 ...Phosphoribosylformylglycinamidine synthase PurL / Phosphoribosylformylglycinamidine synthase, N-terminal / Formylglycinamide ribonucleotide amidotransferase N-terminal / 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
類似検索 - ドメイン・相同性
ADENOSINE-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine synthase
類似検索 - 構成要素
生物種Salmonella typhimurium (サルモネラ菌)
手法X線回折 / 分子置換 / 解像度: 1.8 Å
データ登録者Sharma, N. / Tanwar, A.S. / Anand, R.
資金援助 インド, 1件
組織認可番号国
Department of Science & Technology (DST, India)DST/INT/SOUTH AFRICA/P-04/2014 インド
引用ジャーナル: Acs Catalysis / 年: 2022
タイトル: Mechanism of Coordinated Gating and Signal Transduction in Purine Biosynthetic Enzyme Formylglycinamidine Synthetase.
著者: Sharma, N. / Singh, S. / Tanwar, A.S. / Mondal, J. / Anand, R.
履歴
登録2021年1月15日登録サイト: PDBJ / 処理サイト: PDBJ
改定 1.02022年1月19日Provider: repository / タイプ: Initial release
改定 1.12022年3月2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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
改定 1.22023年11月29日Group: Data collection / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
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

-
集合体

登録構造単位
A: Phosphoribosylformylglycinamidine synthase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)148,49064
ポリマ－142,4811
非ポリマー6,00963
水21,6721203
1


  • 登録構造と同一
  • 登録者が定義した集合体
  • 根拠: native gel electrophoresis
タイプ名称対称操作数
identity operation1_555x,y,z1
単位格子
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

-
要素

-
タンパク質 , 1種, 1分子 A

#1: タンパク質 Phosphoribosylformylglycinamidine synthase / FGAMS / Formylglycinamide ribonucleotide amidotransferase / FGAR-AT


分子量: 142481.359 Da / 分子数: 1 / 変異: N1051A / 由来タイプ: 組換発現
由来: (組換発現) Salmonella typhimurium (サルモネラ菌)
遺伝子: 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, ...遺伝子: 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
発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A0D6F9Y3, phosphoribosylformylglycinamidine synthase

-
非ポリマー , 5種, 1266分子

#2: 化合物 ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / ADP


分子量: 427.201 Da / 分子数: 1 / 由来タイプ: 合成 / 式: C10H15N5O10P2 / コメント: ADP, エネルギー貯蔵分子*YM
#3: 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: 40 / 由来タイプ: 合成 / 式: C3H8O3
#4: 化合物
ChemComp-SO4 / SULFATE ION / 硫酸ジアニオン


分子量: 96.063 Da / 分子数: 19 / 由来タイプ: 合成 / 式: SO4
#5: 化合物 ChemComp-MG / MAGNESIUM ION / マグネシウムジカチオン


分子量: 24.305 Da / 分子数: 3 / 由来タイプ: 合成 / 式: Mg
#6: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 1203 / 由来タイプ: 天然 / 式: H2O

-
詳細

研究の焦点であるリガンドがあるかN

-
実験情報

-
実験

実験手法: X線回折 / 使用した結晶の数: 1

-
試料調製

結晶マシュー密度: 3.1 Å3/Da / 溶媒含有率: 60.3 %
結晶化温度: 298 K / 手法: 蒸気拡散法, ハンギングドロップ法 / 詳細: 2M Ammonium Sulphate

-
データ収集

回折平均測定温度: 120 K / Serial crystal experiment: N
放射光源由来: 回転陽極 / タイプ: Cu FINE FOCUS / 波長: 1.587 Å
検出器タイプ: RIGAKU RAXIS IV++ / 検出器: IMAGE PLATE / 日付: 2019年10月25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: 1.587 Å / 相対比: 1
反射解像度: 1.8→50 Å / Num. obs: 158641 / % possible obs: 100 % / 冗長度: 8 % / Rpim(I) all: 0.023 / Net I/σ(I): 34.5
反射 シェル解像度: 1.8→1.83 Å / Num. unique obs: 7938 / CC1/2: 0.931

-
解析

ソフトウェア
名称バージョン分類
REFMAC5.8.0135精密化
HKL-2000データスケーリング
PDB_EXTRACT3.27データ抽出
HKL-2000データ削減
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: 1T3T

1t3t


解像度: 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 / 交差検証法: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.083 / 立体化学のターゲット値: MAXIMUM LIKELIHOOD
詳細: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
Rfactor反射数%反射Selection details
Rfree0.1625 8052 5.1 %RANDOM
Rwork0.133 ---
obs0.1345 150265 99.78 %-
溶媒の処理イオンプローブ半径: 0.8 Å / 減衰半径: 0.8 Å / VDWプローブ半径: 1.2 Å / 溶媒モデル: MASK
原子変位パラメータBiso 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
精密化ステップサイクル: final / 解像度: 1.8→47.99 Å
タンパク質核酸リガンド溶媒全体
原子数9927 0 371 1203 11501
Biso mean--46.53 29.83 -
残基数----1290
拘束条件
Refine-IDタイプDev idealDev ideal target数
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精密化 シェル解像度: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
Rfactor反射数%反射
Rfree0.228 568 -
Rwork0.194 11080 -
all-11648 -
obs--99.88 %

+
万見について

-
お知らせ

-
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

-
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

+
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

+
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

+
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。

-
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