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- PDB-7a20: Azobenzene-Based Inhibitors for Tryptophan Synthase -

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基本情報

登録情報
データベース: PDB / ID: 7a20
タイトルAzobenzene-Based Inhibitors for Tryptophan Synthase
要素Tryptophan synthase alpha chain,Tryptophan synthase beta chain
キーワードANTIBIOTIC / antibiotics / enzymes / inhibitors / photopharmacology / photoswitches
機能・相同性
機能・相同性情報


tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / cytosol
類似検索 - 分子機能
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme ...Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
類似検索 - ドメイン・相同性
TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / Tryptophan synthase alpha chain / Tryptophan synthase beta chain / Tryptophan synthase alpha chain
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 / シンクロトロン / 分子置換 / 解像度: 2.5 Å
データ登録者Rajendran, C. / Sterner, R.
資金援助 ドイツ, 1件
組織認可番号国
German Research Foundation (DFG)STE 891/12-1 ドイツ
引用ジャーナル: Chemistry / 年: 2021
タイトル: Towards Photochromic Azobenzene-Based Inhibitors for Tryptophan Synthase.
著者: Simeth, N.A. / Kinateder, T. / Rajendran, C. / Nazet, J. / Merkl, R. / Sterner, R. / Konig, B. / Kneuttinger, A.C.
履歴
登録2020年8月14日登録サイト: PDBE / 処理サイト: PDBE
改定 1.02020年11月4日Provider: repository / タイプ: Initial release
改定 1.12021年3月3日Group: Database references / カテゴリ: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
改定 1.22021年8月4日Group: Derived calculations
カテゴリ: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.assembly_id / _pdbx_struct_assembly_gen.oper_expression
改定 1.32024年5月15日Group: Data collection / Database references / カテゴリ: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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構造の表示

構造ビューア分子:
MolmilJmol/JSmol

ダウンロードとリンク

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集合体

登録構造単位
A: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
B: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
C: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
D: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)306,1158
ポリマ－305,8244
非ポリマー2904
水81145
1
A: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
B: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
ヘテロ分子

C: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
D: Tryptophan synthase alpha chain,Tryptophan synthase beta chain
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)306,1158
ポリマ－305,8244
非ポリマー2904
水724
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_544-x,y-1/2,-z-1/21
Buried area9330 Å2
ΔGint-48 kcal/mol
Surface area45340 Å2
手法PISA
単位格子
Length a, b, c (Å)94.368, 95.968, 184.719
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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要素

#1: タンパク質
Tryptophan synthase alpha chain,Tryptophan synthase beta chain


分子量: 76456.078 Da / 分子数: 4 / 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: trpA, A2O69_02705, A3104_03440, A3111_06745, A3122_00255, A3146_03380, A3R41_00165, A3S30_00165, A3T21_03455, A3T81_00165, A3U32_00150, A3V03_00165, A3V89_11045, A3W57_00165, A3W75_00165, ...遺伝子: trpA, A2O69_02705, A3104_03440, A3111_06745, A3122_00255, A3146_03380, A3R41_00165, A3S30_00165, A3T21_03455, A3T81_00165, A3U32_00150, A3V03_00165, A3V89_11045, A3W57_00165, A3W75_00165, A3W86_01965, A3X15_04675, A3X55_12365, A3Y76_02020, A3Z96_03140, A4J27_03515, A4N07_00165, A4O05_04690, A4O41_00150, A4R48_02635, A6D61_00170, A9C21_03190, A9T39_18105, A9U46_07410, A9U64_18365, AAA76_00150, AAB27_09270, AAB39_14810, AAB79_17605, AAC08_07455, AAC35_00165, AAC42_18410, AAC44_05105, AAC95_06065, AAC98_13025, AAP89_02040, AAQ24_17995, AB424_02950, ABO94_19165, ABP11_12170, ABP54_18790, ABP87_03850, ABQ69_14875, ADQ28_02555, ADQ45_00240, AE787_02705, AF480_03970, AF488_06010, AF489_02665, AF497_08115, AGC55_13730, AGM99_16795, AGQ32_20570, AH984_18390, AHN93_02390, AIC76_02220, AKH62_04250, AKH68_02485, AKI16_02905, AL144_16655, AL151_17295, AL154_21000, AL166_18245, AL168_15620, AL170_16745, AL174_09875, AL184_20195, APP08_15525, APY91_03770, AQ530_01185, AS118_02485, AT354_12420, AU613_22480, AU805_00165, AU830_08695, AU839_18250, AU951_15150, AU965_03075, AVA38_22265, AVB77_10095, AVB94_04695, AVC05_15210, AVC09_12505, AVD08_21490, AVD75_00165, AVD94_08010, AVG17_00165, AVL02_12425, AVL16_02485, AVM19_00175, AWT30_03275, AXM10_01875, AXM23_01440, AXR84_21845, AXU58_18715, AXX99_00240, B1265_17725, B1398_17375, B1642_03095, B1B86_18920, B1B89_03520, B1I91_02735, B1P38_14645, B1Q82_16840, B2E31_01135, B4V59_01135, B4W90_02485, B5A40_16835, B6362_18045, B6G98_13730, B6M25_03795, B6M43_05330, B7071_04190, B7890_00175, B7J30_16895, B7Q27_19120, B8Y16_01435, B8Y36_00155, B8Z46_02485, B9653_00865, B9C61_00150, B9C71_05000, B9C90_02620, B9C91_02590, B9C96_00165, B9M14_03095, B9O84_04985, B9U29_02985, BBQ66_00240, BEL47_09235, BFE55_13565, BFE61_16675, BGP52_00165, BIC00_16195, BIC01_10580, BIC03_16625, BIC13_14195, BJP89_17195, BK110_16900, BKM50_00475, BLB03_15980, BMG85_08675, BMS46_07365, BMU56_00240, BSC80_03845, BSD55_03840, BZ203_00605, BZ210_00240, BZG47_02665, BZN20_03405, BZZ88_16725, C4E88_03760, C5U54_03945, C5W43_02665, CA117_01345, CB102_03620, CB119_10845, CB161_01680, CB198_15690, CB380_00165, CB383_15120, CB416_01750, CB530_00165, CB535_01775, CB570_06130, CB646_05190, CB657_17400, CBH20_00175, CBM40_00165, CBM67_00165, CBM76_00165, CBN77_01660, CBO42_03385, CBR08_18060, CBU32_02805, CBZ90_16170, CC339_09500, CC403_14740, CC453_16025, CC594_08910, CC652_03220, CC725_00150, CC886_03025, CC918_08535, CC944_16230, CC971_02325, CCF93_01195, CCP17_15500, CCW27_18535, CD48_01250, CD977_00550, CDJ75_00180, CDT37_16830, CDZ72_11625, CE355_01005, CE615_00485, CE70_00970, CE806_19050, CE87_00485, CE896_13660, CEC46_02430, CEC56_00175, CED07_00240, CEQ70_19135, CER60_14705, CER78_02655, CET98_00485, CEY64_04075, CFB16_19755, CFB28_02665, CFE76_03605, CFE79_19510, CFF58_02665, CFF59_02525, CFJ48_19420, CGG73_00630, CHN22_02485, CI444_00485, CIX60_05920, CJC42_00250, CPR79_00165, CPS79_00170, CPX68_00150, CQE35_02200, CQG18_02720, CQO33_05130, CR370_00805, CRB02_00250, CSG22_09805, CTJ81_13370, CVR97_02980, D3147_03405, D3174_02065, D3F31_17940, D3T68_17465, D3Y48_10480, D4361_01915, D4369_03490, D4380_02475, D4387_05635, D4422_03585, D4E62_00150, D4E68_07205, D4E74_05085, D4X64_05240, D4X79_00155, D4Y62_02075, D5823_04015, D5949_01700, D5B48_00165, D5C67_05335, D5C71_03580, D5N86_03365, D5N95_03775, D5O82_00165, D5P17_00170, D5X47_00150, D5Y28_01995, D6360_05130, D6367_06235, D6371_00165, D6373_01595, D6395_18515, D6421_01595, D6422_13005, D6J79_06095, D6K10_14630, D6P67_05625, D6Q64_00165, D6S43_00165, D6T00_04260, D6T40_02400, D7F20_01775, D7H43_22435, D7N92_00165, D7O44_03135, D8Q90_00150, D8S24_03725, D9O84_00165, DD95_04145, DJ388_09095, DJ702_07165, DK061_00165, DK631_13465, DK641_13520, DK642_09860, DK689_04165, DK696_00150, DK698_07510, DKJ10_06065, DKR95_00175, DKS55_13070, DKU45_00165, DKU57_01735, DKU80_09485, DLB14_00165, DLB57_04215, DLB93_03780, DLR28_07050, DM322_07700, DMI89_03520, DMO92_04580, DMV40_19515, DMZ93_09320, DN165_02740, DN204_04800, DN359_09810, DN904_05240, DNB97_02890, DNL62_13145, DNM27_00165, DNM63_00165, DNU59_01730, DNV08_02460, DNV12_06765, DNV30_02645, DNY92_05155, DNZ37_13565, DO350_14190, DO533_00150, DO585_06990, DO640_03040, DO698_02860, DO766_01990, DO828_00165, DO960_02185, DOC60_08275, DOH72_01750, DOI32_03375, DOI53_01965, DOI92_02215, DOJ39_00165, DOJ91_00995, DOQ54_00160, DOQ88_05390, DOR12_01815, DOV43_07015, DOW25_01945, DP680_05135, DPB42_18060, DPB45_01835, DPB48_03655, DPB57_00470, DPD91_03680, DPD95_01730, DPD99_16165, DPF41_04660, DPF68_00165, DPK32_00170, DPK79_00165, DPL02_00245, DPP94_16890, DPP97_00165, DPS76_03535, DPT18_00165, DPU20_00150, DPY58_03125, DQ848_22180, DQ947_07370, DQ951_00165, DQC39_04655, DQC52_04020, DQD03_00165, DQD22_02710, DQE64_05325, DQE65_07775, DQK42_00165, DQQ98_01485, DQR10_06595, DQR44_00155, DQR61_14685, DQS14_15275, DQY10_00175, DQZ46_17880, DQZ56_00165, DR982_04290, DRL45_00165, DRM14_00165, DRM16_05695, DRR75_10995, DRT38_04265, DRT61_09470, DRT65_11175, DRV05_00150, DRW84_00160, DRX66_18265, DS270_00160, DS296_18550, DS451_00160, DS453_03510, DS521_00165, DS619_01750, DSF69_00165, DSF94_07465, DSG41_00165, DSM38_03595, DSN15_07075, DSR36_00150, DTE73_04565, DTF68_04450, DTG22_18830, DTG27_10390, DTW13_02010, DTW14_04720, DTW26_04250, DU071_15075, DU223_01835, DU657_05890, DU821_03570, DU879_04025, DU924_01705, DUQ28_05205, DUQ56_02015, DUQ92_13425, DUR36_02790, DUV75_02775, DUW10_00165, DUW48_00165, DVF14_00165, DVF88_01725, DVG01_03395, DVZ53_00975, DWU22_05275, DY580_18355, DYM27_15965, DYS82_04400, DZG11_04030, E0584_04235, E0595_03330, E0935_04470, E0989_02695, E0M34_03825, E0U75_00170, E0V94_01720, E1A11_00170, E1A20_21775, E5196_00315, E6W45_19445, EBB93_00165, EBC01_00250, EBD14_01910, EBD99_05485, EBK21_00170, EBL31_00490, EBO41_01945, EBP31_03915, EC404_00170, EC52_01135, ECA50_02905, ECC89_03730, ED424_01895, ED467_02970, EDL18_05825, EEK73_02635, EEQ30_08390, EER35_12060, EGL32_03685, EGN81_18585, EGU67_04970, EGU98_07510, EHB09_01395, EHB24_02710, EHB55_00165, EHC98_05580, EIE48_00170, EIW53_01740, EJI18_00155, EJO08_03325, EJO98_00565, EKA25_00510, EL822_00175, ELO47_03140, ELR28_01915, ELS01_00155, EM832_04940, EM840_00165, EMN66_03650, EMY79_01615, EO190_03990, EP115_03025, EP446_10220, EPB30_00170, EPH81_02040, EQG93_01815, EQG94_00165, ERM04_00170, EU306_00165, EU349_00155, EU873_02915, EUB95_14525, EUQ56_04025, EUQ65_02365, EUQ74_06790, EUS13_04110, EVY71_00180, EW905_13420, EWB18_18055, EWE52_00155, EWJ47_00250, EWZ09_03885, EXA47_00250, EXB31_22555, EXB41_01725, EYA29_11485, EYJ91_04470, F0D96_02435, F2O93_00605, F2P00_03530, F3Q46_10710, F3Q58_08080, F3Q59_08000, F3Q88_02705, F3Q97_02930, F3R12_00170, F3R61_03870, F3R63_00160, F7773_04550, F9G02_00150, F9O44_16545, FE758_04145, FEM52_02630, FGZ46_01675, FJM64_00165, FL833_00150, FQC24_03100, FQD13_06725, GCH31_00150, GCQ81_00165, GEZ01_04015, GW08_03170, JO10_00485, KP44_16040, LZ63_02665, NG02_04170, NG06_16725, NG18_14005, NU83_02665, QA89_14460, QB40_00165, QD15_05220, R035_09170, RJ78_16495, SAMEA4398682_02246, SE14_01811, Y934_00970, YG50_13190, YR17_00165, Z700_00165, ZB89_05450, ZC54_00165, ZT09_07605, ZT28_00160, ZT74_16545, ZT89_11220, ZU86_12130, ZU92_17275, ZV06_15530, ZV17_18190, ZV33_00160, ZV34_00165, ZV38_00165, ZV58_05875, ZV70_10430, ZV76_15960, ZV78_00160, ZV90_13180, ZW74_18835, ZX03_08395, ZY23_01875, ZY27_00165, ZY40_08865, ZY51_17020, ZZ18_11975, ZZ43_16745, ZZ77_00150, ZZ79_17010, trpB, A2O69_02700, A3104_03435, A3111_06740, A3122_00260, A3146_03375, A3R41_00170, A3S30_00170, A3T21_03460, A3T81_00170, A3U32_00155, A3V03_00170, A3V89_11050, A3W57_00170, A3W86_01970, A3X15_04680, A3X55_12370, A3Y76_02015, A3Z96_03135, A4J27_03520, A4N07_00170, A4O05_04695, A4O41_00155, A4R48_02630, A6D61_00175, A9C21_03185, A9T39_18110, A9U46_07415, A9U64_18370, AAA76_00155, AAB27_09275, AAB39_14815, AAB79_17610, AAC08_07460, AAC35_00170, AAC42_18415, AAC44_05110, AAC95_06070, AAC98_13030, AAP89_02045, AAQ24_18000, AB424_02945, ABO94_19170, ABP11_12175, ABP54_18795, ABP87_03855, ABQ69_14880, ADQ28_02550, ADQ45_00245, AE787_02700, AF480_03975, AF488_06015, AF489_02660, AF497_08120, AGC55_13735, AGM99_16800, AGQ32_20575, AH984_18395, AHN93_02395, AIC76_02215, AKH62_04245, AKH68_02480, AKI16_02910, AL144_16660, AL151_17300, AL166_18250, AL168_15625, AL170_16750, AL174_09880, AL184_20200, APP08_15530, APY91_03765, AQ530_01180, AS118_02480, AT354_12415, AU613_22485, AU805_00170, AU830_08700, AU839_18255, AU951_15155, AU965_03080, AVA38_22260, AVB77_10100, AVB94_04700, AVC05_15215, AVD75_00170, AVD94_08015, AVG17_00170, AVL02_12430, AVL16_02480, AVM19_00180, AWT30_03270, AXM10_01880, AXM23_01435, AXR84_21850, AXU58_18720, AXX99_00245, B1265_17730, B1398_17380, B1642_03090, B1B86_18925, B1B89_03525, B1I91_02730, B1P38_14650, B1Q82_16845, B2E31_01130, B4V59_01130, B4W90_02480, B5A40_16840, B6362_18050, B6G98_13735, B6M25_03790, B6M43_05335, B7071_04185, B7890_00180, B7J30_16900, B7Q27_19125, B8Y16_01430, B8Y36_00160, B8Z46_02480, B9653_00860, B9C61_00155, B9C71_05005, B9C90_02615, B9C91_02585, B9C96_00170, B9M14_03090, B9O84_04980, B9U29_02980, BBQ66_00245, BEL47_09240, BFE55_13570, BFE61_16680, BGP52_00170, BIC00_16200, BIC01_10585, BIC03_16630, BIC13_14200, BJP89_17200, BK110_16905, BKM50_00480, BLB03_15985, BMG85_08680, BMS46_07360, BMU56_00245, BSC80_03850, BSD55_03835, BZ203_00610, BZ210_00245, BZG47_02660, BZN20_03410, BZZ88_16730, C4E88_03765, C5W43_02660, CA117_01340, CB102_03625, CB119_10850, CB161_01685, CB198_15695, CB380_00170, CB383_15125, CB416_01745, CB530_00170, CB535_01780, CB570_06135, CB646_05195, CB657_17405, CBH20_00180, CBM40_00170, CBM67_00170, CBM76_00170, CBN77_01665, CBO42_03390, CBR08_18065, CBU32_02810, CBZ90_16175, CC339_09505, CC403_14745, CC453_16030, CC594_08915, CC652_03225, CC725_00155, CC886_03030, CC918_08540, CC944_16235, CC971_02330, CCF93_01200, CCP17_15505, CCW27_18540, CD48_01255, CD977_00555, CDJ75_00185, CDT37_16835, CDZ72_11630, CE355_01000, CE615_00490, CE70_00965, CE806_19055, CE87_00490, CE896_13665, CEC46_02425, CEC56_00180, CED07_00245, CEQ70_19140, CER60_14710, CER78_02650, CET98_00490, CEY64_04070, CFB16_19760, CFB28_02660, CFE76_03600, CFE79_19515, CFF58_02660, CFF59_02520, CFJ48_19425, CGG73_00635, CHN22_02480, CI444_00490, CIX60_05915, CJC42_00255, CPR79_00170, CPS79_00175, CPX68_00155, CQE35_02195, CQG18_02715, CQO33_05135, CR370_00800, CR439_06560, CRB02_00255, CSG22_09800, CTJ81_13375, CVR97_02985, D3147_03410, D3174_02070, D3F31_17945, D3T68_17470, D3Y48_10485, D4361_01920, D4369_03495, D4380_02480, D4387_05640, D4422_03590, D4E62_00155, D4E68_07210, D4E74_05090, D4X64_05245, D4X79_00160, D4Y62_02080, D5823_04020, D5949_01705, D5B48_00170, D5C67_05340, D5C71_03585, D5N86_03370, D5N95_03780, D5O82_00170, D5P17_00175, D5X47_00155, D5Y28_02000, D6360_05135, D6367_06240, D6371_00170, D6373_01600, D6395_18520, D6421_01600, D6422_13010, D6J79_06100, D6K10_14635, D6P67_05630, D6Q64_00170, D6S43_00170, D6T00_04265, D6T40_02405, D7F20_01770, D7H43_22440, D7N92_00170, D7O44_03140, D8Q90_00155, D8S24_03730, D9O84_00170, DD95_04150, DJ388_09100, DJ702_07170, DK061_00170, DK631_13470, DK641_13525, DK642_09865, DK689_04170, DK696_00155, DK698_07515, DKJ10_06070, DKR95_00180, DKS55_13075, DKU45_00170, DKU57_01740, DKU80_09490, DLB14_00170, DLB57_04220, DLB93_03785, DLR28_07055, DM322_07705, DMO92_04585, DMV40_19520, DMZ93_09325, DN165_02735, DN204_04805, DN359_09815, DN904_05235, DNB97_02885, DNL62_13150, DNM27_00170, DNM63_00170, DNU59_01735, DNV08_02465, DNV12_06770, DNV30_02640, DNY92_05160, DNZ37_13570, DO350_14195, DO533_00155, DO585_06995, DO640_03045, DO698_02865, DO766_01995, DO828_00170, DO960_02190, DOC60_08280, DOH72_01755, DOI32_03380, DOI53_01970, DOI92_02220, DOJ39_00170, DOJ91_01000, DOQ54_00165, DOQ88_05395, DOR12_01820, DOV43_07020, DOW25_01950, DP680_05140, DPB42_18065, DPB45_01840, DPB48_03660, DPB57_00475, DPD91_03685, DPD95_01735, DPD99_16170, DPF41_04665, DPF68_00170, DPK32_00175, DPK79_00170, DPL02_00250, DPP94_16895, DPP97_00170, DPS76_03540, DPT18_00170, DPU20_00155, DPY58_03130, DQ848_22185, DQ947_07375, DQ951_00170, DQC39_04660, DQC52_04025, DQD03_00170, DQD22_02705, DQE64_05330, DQE65_07780, DQK42_00170, DQQ98_01490, DQR10_06600, DQR44_00160, DQR61_14690, DQS14_15280, DQY10_00180, DQZ46_17885, DQZ56_00170, DR982_04285, DRL45_00170, DRM14_00170, DRM16_05700, DRR75_11000, DRT38_04270, DRT61_09475, DRT65_11180, DRV05_00155, DRW84_00165, DRX66_18270, DS270_00165, DS296_18555, DS451_00165, DS453_03515, DS521_00170, DS619_01755, DSF69_00170, DSF94_07470, DSG41_00170, DSM38_03600, DSN15_07080, DSR36_00155, DTE73_04570, DTF68_04455, DTG22_18835, DTG27_10395, DTW13_02015, DTW14_04725, DTW26_04255, DU071_15080, DU223_01840, DU657_05885, DU821_03575, DU879_04030, DU924_01710, DUQ28_05210, DUQ56_02020, DUQ92_13430, DUR36_02795, DUV75_02780, DUW10_00170, DUW48_00170, DVF14_00170, DVG01_03400, DVZ53_00970, DWU22_05270, DY580_18360, DYM27_15970, DYS82_04405, DZG11_04025, E0595_03335, E0935_04475, E0989_02690, E0M34_03830, E0U75_00175, E0V94_01725, E1A11_00175, E1A20_21780, E5196_00320, E6W45_19450, EBB93_00170, EBC01_00255, EBD14_01915, EBD99_05490, EBK21_00175, EBL31_00495, EBO41_01950, EBP31_03920, EC404_00175, EC52_01130, ECA50_02910, ECC89_03735, ED424_01900, ED467_02975, EDL18_05830, EEK73_02630, EEQ30_08395, EER35_12065, EGL32_03690, EGN81_18590, EGU67_04975, EGU98_07515, EHB09_01390, EHB24_02705, EHB55_00170, EHC98_05585, EIE48_00175, EIW53_01745, EJI18_00160, EJO08_03330, EJO98_00570, EKA25_00505, EL822_00180, ELO47_03135, ELR28_01920, ELS01_00160, EM832_04945, EM840_00170, EMN66_03645, EMY79_01620, EO190_03995, EP115_03030, EP446_10225, EPB30_00175, EPH81_02045, EQG93_01820, EQG94_00170, ERM04_00175, EU306_00170, EU349_00160, EU873_02910, EUB95_14530, EUQ56_04030, EUQ65_02370, EUQ74_06795, EUS13_04115, EVY71_00185, EW905_13425, EWB18_18060, EWE52_00160, EWJ47_00255, EWZ09_03890, EXA47_00255, EXB41_01730, EYA29_11490, EYJ91_04475, F0D96_02430, F2O93_00610, F2P00_03525, F3Q46_10715, F3Q58_08085, F3Q59_08005, F3Q88_02710, F3Q97_02935, F3R12_00175, F3R61_03875, F3R63_00165, F7773_04555, F9G02_00155, F9O44_16550, FE758_04150, FEM52_02625, FGZ46_01680, FJM64_00170, FL833_00155, FQC24_03095, FQD13_06720, FQX78_06105, GCH31_00155, GCQ81_00170, GCZ80_03085, GEZ01_04020, GW08_03175, JO10_00490, KP44_16045, LZ63_02660, NG02_04175, NG06_16730, NG18_14010, NU83_02660, QA89_14465, QB40_00170, QD15_05225, R035_09175, RJ78_16500, SAMEA4398682_02247, SE14_01810, Y934_00965, YG50_13195, YR17_00170, YT65_03520, Z700_00170, ZB89_05455, ZC54_00170, ZT09_07610, ZT28_00165, ZT74_16550, ZT89_11225, ZU86_12135, ZU92_17280, ZV06_15535, ZV17_18195, ZV33_00165, ZV34_00170, ZV38_00170, ZV58_05880, ZV70_10435, ZV76_15965, ZV78_00165, ZV90_13185, ZW74_18840, ZX03_08400, ZY23_01880, ZY27_00170, ZY40_08870, ZY51_17025, ZZ18_11980, ZZ43_16750, ZZ77_00155, ZZ79_17015
発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A0D6FWC1, UniProt: A0A0F7J6T4, UniProt: P00929*PLUS, tryptophan synthase
#2: 化合物 ChemComp-NA / SODIUM ION / ナトリウムカチオン


分子量: 22.990 Da / 分子数: 2 / 由来タイプ: 合成 / 式: Na / タイプ: SUBJECT OF INVESTIGATION
#3: 化合物 ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM / メチルトリス(ヒドロキシメチル)アミニウム


分子量: 122.143 Da / 分子数: 2 / 由来タイプ: 合成 / 式: C4H12NO3 / タイプ: SUBJECT OF INVESTIGATION
#4: 水 ChemComp-HOH / water


分子量: 18.015 Da / 分子数: 45 / 由来タイプ: 天然 / 式: H2O
研究の焦点であるリガンドがあるかY

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実験情報

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実験

実験手法: X線回折 / 使用した結晶の数: 1

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試料調製

結晶化温度: 291 K / 手法: 蒸気拡散法 / 詳細: PEG 8000, 0.1 M sodium citrate

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データ収集

回折平均測定温度: 100 K / Serial crystal experiment: N
放射光源由来: シンクロトロン / サイト: SLS / ビームライン: X06DA / 波長: 1 Å
検出器タイプ: DECTRIS PILATUS 300K / 検出器: PIXEL / 日付: 2019年2月13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 Å / 相対比: 1
反射解像度: 2.5→47.1 Å / Num. obs: 58178 / % possible obs: 99.7 % / 冗長度: 13.5 % / CC1/2: 0.99 / CC star: 1 / Net I/σ(I): 12.8
反射 シェル解像度: 2.5→2.59 Å / Num. unique obs: 5652 / CC1/2: 0.65 / CC star: 0.88

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解析

ソフトウェア
名称バージョン分類
PHENIX1.17精密化
XDSデータ削減
XSCALEデータスケーリング
PHASER位相決定
精密化構造決定の手法: 分子置換
開始モデル: x

解像度: 2.5→47.1 Å / 交差検証法: FREE R-VALUE
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.25 --
Rwork0.19 --
obs-58178 99.7 %
原子変位パラメータBiso mean: 66.8 Å2
精密化ステップサイクル: LAST / 解像度: 2.5→47.1 Å
タンパク質核酸リガンド溶媒全体
原子数9712 0 18 45 9775
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.01049939
X-RAY DIFFRACTIONf_angle_d1.092713464
X-RAY DIFFRACTIONf_chiral_restr0.05421504
X-RAY DIFFRACTIONf_plane_restr0.00621782
X-RAY DIFFRACTIONf_dihedral_angle_d20.81613653

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万見について

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お知らせ

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2022年2月9日: EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

EMDBエントリの付随情報ファイルのフォーマットが新しくなりました

  • EMDBのヘッダファイルのバージョン3が、公式のフォーマットとなりました。
  • これまでは公式だったバージョン1.9は、アーカイブから削除されます。

関連情報:EMDBヘッダ

外部リンク:wwPDBはEMDBデータモデルのバージョン3へ移行します

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2020年8月12日: 新型コロナ情報

新型コロナ情報

URL: https://pdbj.org/emnavi/covid19.php

新ページ: EM Navigatorに新型コロナウイルスの特設ページを開設しました。

関連情報:Covid-19情報 / 2020年3月5日: 新型コロナウイルスの構造データ

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2020年3月5日: 新型コロナウイルスの構造データ

新型コロナウイルスの構造データ

関連情報:万見生物種 / 2020年8月12日: 新型コロナ情報

外部リンク:COVID-19特集ページ - PDBj / 今月の分子2020年2月：コロナウイルスプロテーアーゼ

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2019年1月31日: EMDBのIDの桁数の変更

EMDBのIDの桁数の変更

  • EMDBエントリに付与されているアクセスコード(EMDB-ID)は4桁の数字(例、EMD-1234)でしたが、間もなく枯渇します。これまでの4桁のID番号は4桁のまま変更されませんが、4桁の数字を使い切った後に発行されるIDは5桁以上の数字(例、EMD-12345)になります。5桁のIDは2019年の春頃から発行される見通しです。
  • EM Navigator/万見では、接頭語「EMD-」は省略されています。

関連情報:Q: 「EMD」とは何ですか？ / 万見/EM NavigatorにおけるID/アクセスコードの表記

外部リンク:EMDB Accession Codes are Changing Soon! / PDBjへお問い合わせ

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2017年7月12日: PDB大規模アップデート

PDB大規模アップデート

  • 新バージョンのPDBx/mmCIF辞書形式に基づくデータがリリースされました。
  • 今回の更新はバージョン番号が4から5になる大規模なもので、全エントリデータの書き換えが行われる「Remediation」というアップデートに該当します。
  • このバージョンアップで、電子顕微鏡の実験手法に関する多くの項目の書式が改定されました(例：em_softwareなど)。
  • EM NavigatorとYorodumiでも、この改定に基づいた表示内容になります。

外部リンク:wwPDB Remediation / OneDepデータ基準に準拠した、より強化された内容のモデル構造ファイルが、PDBアーカイブで公開されました。

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万見 (Yorodumi)

幾万の構造データを、幾万の視点から

  • 万見(Yorodumi)は、EMDB/PDB/SASBDBなどの構造データを閲覧するためのページです。
  • EM Navigatorの詳細ページの後継、Omokage検索のフロントエンドも兼ねています。

関連情報:EMDB / PDB / SASBDB / 3つのデータバンクの比較 / 万見検索 / 2016年8月31日: 新しいEM Navigatorと万見 / 万見文献 / Jmol/JSmol / 機能・相同性情報 / 新しいEM Navigatorと万見の変更点

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