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- PDB-7lce: Structure of D-Glucosaminate-6-phosphate Ammonia-lyase -

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基本情報

登録情報
データベース: PDB / ID: 7lce
タイトルStructure of D-Glucosaminate-6-phosphate Ammonia-lyase
要素D-glucosaminate-6-phosphate ammonia lyase
キーワードLYASE (リアーゼ) / Aminotransferase fold / D-glucosaminate metabolism
機能・相同性D-glucosaminate-6-phosphate ammonia lyase DgaE-like / L-seryl-tRNA selenium transferase-like / L-seryl-tRNA selenium transferase / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / lyase activity / D-glucosaminate-6-phosphate ammonia lyase
機能・相同性情報
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: 2.58 Å
データ登録者Phillips, R.S.
資金援助 米国, 1件
組織認可番号国
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM137008 米国
引用ジャーナル: Biochemistry / 年: 2021
タイトル: Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical ...タイトル: Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid.
著者: Phillips, R.S. / Ting, S.C. / Anderson, K.
履歴
登録2021年1月10日登録サイト: RCSB / 処理サイト: RCSB
改定 1.02021年6月9日Provider: repository / タイプ: Initial release
改定 1.12023年10月18日Group: Data collection / Database references / Refinement description
カテゴリ: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
改定 1.22023年11月15日Group: Data collection / カテゴリ: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: D-glucosaminate-6-phosphate ammonia lyase
B: D-glucosaminate-6-phosphate ammonia lyase
C: D-glucosaminate-6-phosphate ammonia lyase
D: D-glucosaminate-6-phosphate ammonia lyase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)159,48626
ポリマ－158,3764
非ポリマー1,11022
水2,702150
1
A: D-glucosaminate-6-phosphate ammonia lyase
B: D-glucosaminate-6-phosphate ammonia lyase
C: D-glucosaminate-6-phosphate ammonia lyase
D: D-glucosaminate-6-phosphate ammonia lyase
ヘテロ分子

A: D-glucosaminate-6-phosphate ammonia lyase
B: D-glucosaminate-6-phosphate ammonia lyase
C: D-glucosaminate-6-phosphate ammonia lyase
D: D-glucosaminate-6-phosphate ammonia lyase
ヘテロ分子


分子量 (理論値)分子数
合計 (水以外)318,97252
ポリマ－316,7528
非ポリマー2,22044
水1448
タイプ名称対称操作数
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
単位格子
Length a, b, c (Å)60.374, 171.569, 195.054
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDモデル要素
11B-526-

HOH

21C-513-

HOH

31D-544-

HOH

非結晶学的対称性 (NCS)NCSドメイン:
IDEns-ID詳細
d_1ens_1(chain "A" and (resid 1 through 165 or resid 167...
d_2ens_1(chain "B" and (resid 1 through 165 or resid 167...
d_3ens_1(chain "C" and (resid 1 through 165 or resid 167...
d_4ens_1(chain "D" and (resid 1 through 165 or resid 167...

NCSドメイン領域:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METVALA1 - 165
d_12ens_1LYSASNA167 - 182
d_13ens_1LEUGLYA184 - 225
d_14ens_1LYSASPA227 - 369
d_15ens_1DMSDMSB
d_21ens_1METVALE1 - 165
d_22ens_1LYSASNE167 - 182
d_23ens_1LEUGLYE184 - 225
d_24ens_1LYSASPE227 - 369
d_25ens_1DMSDMSF
d_31ens_1METVALG1 - 165
d_32ens_1LYSASNG167 - 182
d_33ens_1LEUGLYG184 - 225
d_34ens_1LYSASPG227 - 369
d_35ens_1DMSDMSH
d_41ens_1METVALI1 - 165
d_42ens_1LYSASNI167 - 182
d_43ens_1LEUGLYI184 - 225
d_44ens_1LYSASPI227 - 369
d_45ens_1DMSDMSJ

NCS oper:
IDCodeMatrixベクター
1given(0.752579837329, -0.510752802861, -0.415638259566), (0.495035510927, 0.0225923228966, 0.868578971578), (-0.434238910472, -0.859430719323, 0.269843301412)51.934654045, -12.4965228604, 88.3336672872
2given(-0.735913447788, -0.508634541973, 0.446903009698), (-0.499903250097, -0.0369923255324, -0.865290880799), (0.456648812445, -0.860187462454, -0.22704491082)54.2321070732, 104.801909316, 86.5632097877
3given(-0.51145772372, 0.0213046501672, 0.859044299631), (0.020890589657, -0.999088874237, 0.03721565046), (0.859054468652, 0.0369801738318, 0.510546654707)1.66155348856, 90.2939908468, -3.08176810246

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要素

#1: タンパク質
D-glucosaminate-6-phosphate ammonia lyase / Selenocysteine synthase / Transferase


分子量: 39593.957 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: selA_2, dgaE, A3104_21605, A3111_09960, A3122_12735, A3146_15045, A3R41_07565, A3S30_02955, A3T21_08030, A3T81_03495, A3U32_14755, A3V03_16095, A3V89_00235, A3W57_03380, A3W75_06435, A3W86_ ...遺伝子: selA_2, dgaE, A3104_21605, A3111_09960, A3122_12735, A3146_15045, A3R41_07565, A3S30_02955, A3T21_08030, A3T81_03495, A3U32_14755, A3V03_16095, A3V89_00235, A3W57_03380, A3W75_06435, A3W86_04545, A3X15_00235, A3X55_04110, A3Y76_07350, A3Z96_04130, A4J27_00240, A4N07_07395, A4O05_16705, A4O41_15960, A4R48_20285, A6D61_11415, A9C21_08165, A9T39_10340, A9U46_05925, A9U64_14215, AAA76_11240, AAB27_10705, AAB39_09580, AAC08_22375, AAC35_03015, AAC42_07475, AAC44_12965, AAC98_15720, AAQ24_10865, AB424_07565, ABO94_07150, ABP87_07705, ADQ28_15815, ADQ45_06130, AE787_04130, AF480_11215, AF488_12465, AF489_14925, AF497_03560, AGC55_05030, AGM99_04990, AGQ32_00230, AH984_08495, AHN93_11520, AIC76_13770, AKH62_08615, AKH68_15555, AKI16_07535, APY91_09970, AQ530_12475, AS118_05705, AT354_07990, AU613_17865, AU805_03345, AU830_11590, AU839_08945, AU951_10085, AU965_14750, AVA38_16490, AVB77_06395, AVB94_01990, AVC05_03285, AVC09_05420, AVD08_07985, AVD75_06905, AVD94_10420, AVG17_05175, AVL02_11640, AVL16_06920, AVM19_07240, AWT30_07820, AXM10_00235, AXM23_11675, AXR84_06650, AXU58_07370, AXX99_20725, B1265_04750, B1398_07865, B1642_06605, B1B86_06895, B1B89_06400, B1I91_10675, B1P38_09445, B1Q82_13995, B2E31_11510, B4V59_11225, B4W90_05125, B5A40_02630, B6362_02605, B6G98_15880, B6M25_05275, B6M43_12740, B7071_05520, B7890_15470, B7J30_00235, B7Q27_04745, B8Y16_02890, B8Y36_14530, B8Z46_05570, B9653_18625, B9M14_04555, B9O84_10005, B9U29_13595, BBQ66_19075, BEL47_14045, BGP52_05050, BIC00_16670, BIC01_11055, BIC03_04280, BIC13_02610, BK110_04945, BKM50_17535, BLB03_07155, BMS46_12040, BMU56_20200, BSC80_11910, BSD55_09105, BZ203_16380, BZ210_08555, BZG47_19060, BZN20_09225, BZZ88_15855, C4E88_12820, C5U54_06940, C5W43_16235, CA117_13580, CB102_20575, CB119_16505, CB161_06635, CB198_11260, CB380_17240, CB383_04725, CB530_02085, CB535_00175, CB570_01230, CB657_00235, CBH20_03930, CBM40_06725, CBM67_03730, CBM76_13060, CBN77_11220, CBO42_00235, CBR08_02610, CBU32_01115, CBZ90_15285, CC339_14505, CC403_03575, CC453_00230, CC594_06105, CC886_09390, CC918_00235, CC944_20085, CC971_07645, CCF93_04520, CCP17_05010, CCW27_18020, CD48_04815, CD977_15700, CDJ75_02455, CDT37_05005, CDZ72_00235, CE355_04080, CE615_12255, CE70_04735, CE806_15205, CE87_08585, CE896_21755, CEC46_19125, CEC56_02375, CED07_08930, CEQ70_11170, CER78_03375, CET98_06315, CEY64_14985, CFB16_07970, CFB28_16270, CFE76_08205, CFE79_11130, CFF58_22315, CFF59_19115, CFJ48_05760, CGG73_14400, CHN22_12270, CI444_06460, CIX60_11070, CJC42_10875, CPR79_09105, CPS79_03995, CPX68_05985, CQE35_10530, CQG18_03115, CQO33_02070, CR370_15260, CRB02_10605, CSG22_20575, CVR97_16080, D3147_00235, D3174_05685, D3F31_08530, D3T68_09530, D3Y48_19240, D4361_00240, D4369_00240, D4380_09495, D4387_02320, D4422_07370, D4E62_06310, D4E68_00240, D4E74_02175, D4X64_02180, D4X79_05690, D4Y62_05865, D5823_19415, D5949_13715, D5B48_05005, D5C67_00240, D5C71_11480, D5N86_06955, D5N95_00240, D5O82_09450, D5P17_09065, D5X47_03110, D5Y28_11235, D6360_00275, D6367_02720, D6371_04905, D6373_12445, D6395_00240, D6421_10680, D6422_07120, D6J79_02575, D6K10_09245, D6P67_04165, D6Q64_05870, D6S43_05365, D6T00_07770, D6T40_10725, D7F20_21465, D7H43_10555, D7N92_03130, D7O44_10745, D8Q90_03285, D8S24_00240, D9O84_05575, DD95_07090, DJ388_10345, DJ702_11425, DK061_06395, DK631_10775, DK641_05920, DK642_07845, DK696_05345, DK698_11005, DKJ10_10855, DKR95_03040, DKS55_07075, DKU45_07400, DKU57_08220, DKU80_11340, DLB14_09155, DLB57_06490, DLB93_00240, DLR28_04025, DM322_03750, DMI89_17320, DMV40_02585, DMZ93_10670, DN204_11415, DN359_15470, DNB97_16355, DNL62_00235, DNM27_07420, DNM63_05200, DNU59_06600, DNV08_08925, DNV12_22105, DNV30_10245, DNZ37_00240, DO350_15285, DO533_10945, DO585_00240, DO640_00240, DO698_04005, DO828_05535, DO960_18855, DOH72_08010, DOI32_06290, DOI53_00275, DOI92_07580, DOJ91_05370, DOQ54_07505, DOQ88_06595, DOR12_09195, DOV43_01485, DOW25_05970, DP680_00240, DPB45_06940, DPB48_09455, DPD95_04015, DPD99_03130, DPF41_12160, DPF68_05950, DPK32_08430, DPL02_09045, DPP94_11120, DPP97_08450, DPS76_06440, DPT18_06260, DPU20_08250, DPY58_21110, DQ848_00240, DQ947_10795, DQ951_13090, DQC39_12325, DQC52_09065, DQD03_08600, DQE64_00240, DQK42_06135, DQQ98_04505, DQR10_02075, DQR44_03115, DQR61_02270, DQS14_20990, DQY10_19985, DQZ46_16710, DQZ56_05305, DR982_16460, DRL45_03615, DRM14_09020, DRM16_02480, DRR75_12965, DRT61_12205, DRT65_06680, DRV05_06455, DRW84_09175, DRX66_00240, DS270_05005, DS296_13430, DS451_21555, DS453_00240, DS521_06150, DS619_07370, DSF69_08225, DSG41_20795, DSN15_04030, DSR36_08415, DTE73_18135, DTF68_09125, DTG22_04235, DTG27_15945, DTW13_07590, DTW14_13540, DTW26_02575, DU223_00180, DU657_14935, DU821_00240, DU879_06295, DU924_08765, DUQ28_07785, DUQ56_16470, DUQ92_07545, DUR36_07980, DUV75_04770, DUW10_02530, DUW48_08310, DVF14_05050, DVF88_06690, DVG01_08595, DVZ53_15260, DWU22_19055, DY580_08660, DYM27_12345, DYS82_09190, DZG11_15905, E0584_00630, E0595_11110, E0935_00235, E0M34_18235, E0U75_03505, E0V94_06670, E1A11_05265, E5196_07260, E6W45_04890, EBB93_02425, EBC01_13365, EBD14_00240, EBD99_09680, EBK21_05650, EBO41_20635, EBP31_08480, EC404_07450, EC52_14135, ECC89_00240, ED424_06825, ED467_10440, EDL18_02440, EEK73_11800, EEQ30_13355, EER35_18550, EGL32_09475, EGN81_05445, EGU67_11330, EHB09_17235, EHB55_10585, EHC98_02435, EIE48_09040, EIW53_10020, EJI18_05270, EJO08_11050, EJO98_16350, EKA25_11620, EL822_05540, ELO47_13095, ELR28_06650, ELS01_05755, EM832_11295, EM840_09780, EMN66_04645, EMY79_15795, EO190_18975, EP115_07090, EP446_06715, EPB30_05540, EPH81_06660, EQG93_07825, EQG94_09250, ERM04_03100, EU306_03130, EU349_07740, EU873_00180, EUQ65_10430, EUQ74_00240, EUS13_02440, EVY71_23275, EW905_00175, EWB18_17085, EWE52_14555, EWJ47_07780, EWZ09_02215, EXA47_08960, EXB31_05605, EXB41_06725, EYA29_07825, EYJ91_20305, F0D96_19290, F2O93_12040, F2P00_06605, F3Q46_04325, F3Q58_02410, F3Q59_06345, F3Q88_01060, F3Q97_07950, F3R12_09345, F3R61_02230, F3R63_05095, F9G02_17445, F9O44_10085, FE758_16315, FJM64_04360, FL833_04125, FQC24_04530, FQD13_14295, G0038_05905, G0040_17515, G0042_11585, G0045_09800, G0047_04965, G0048_08470, G0051_05035, G0052_10225, G0059_05310, G0061_07560, G0062_08145, G0063_08025, G0067_08640, G0069_08215, G0070_17335, G0071_06575, G0072_13865, G0074_09615, G0076_06860, G0077_08400, G0080_10265, G0084_11025, G0086_10525, G0087_08470, G0088_07565, G0089_24050, G0090_03130, G0094_03360, G0100_23465, G0101_07665, G0102_07355, G0111_06985, G0113_08455, G0117_05190, G0123_08470, G0124_08205, G0148_07230, G0157_07885, G0170_09205, G0A05_13435, G0A28_19680, G0A32_12905, G0A39_19405, G0A43_18505, G0A46_20665, G0A50_13145, G0A51_13555, G0A52_20510, G0A60_11970, G0A61_12165, G0A63_10835, G0A67_15570, G0A68_11040, G0A70_12455, G0A76_09550, G0A79_14300, G0A92_05965, G0A97_12565, G0B03_05725, G0B05_02180, G0B07_02085, G0B08_22240, G0B12_00240, G0B96_05695, G0C03_02550, G0C04_06550, G0C34_07930, G0E15_12285, G0E20_21705, G0J24_04435, G0J26_07840, G0J27_01470, G0J28_05610, G0J31_20395, G0J33_04105, G0J34_08885, G0J36_05910, G0J37_08625, G0J40_07450, G0J44_08740, G0J45_05875, G0J46_06385, G0J47_08505, G0J49_06645, G0J50_09345, G0J51_07485, G0J53_02615, G0J55_05325, G0J58_03610, G0J59_15850, G0J62_08675, G0J65_11105, G0J66_02280, G0J67_05475, G0J69_02410, G0J71_02410, G0J73_11645, G0J76_02420, G0J79_18650, G0J81_05100, G0J85_05100, G0J89_11575, G0J92_10820, G0J94_11985, G0J96_10390, G0J97_14955, G0K00_17375, G0K03_06240, G0K04_14270, G0K05_08930, G0K07_02410, G0K10_06835, G0K13_05515, G0K15_04050, G0K16_10760, G0K18_14355, G0K19_03030, G0K20_11195, G0K23_06230, G0K25_00240, G0K26_17405, G0K28_11645, G0K30_05630, G0K31_02225, G0K32_18475, G0K33_05010, G0K37_00240, G0K38_09780, G0K39_15835, G0K41_07335, G0K42_07825, G0K44_16875, G0K46_05100, G0K47_19060, G0K48_10980, G0K49_11770, G0K52_12965, G0K53_13120, G0K56_11430, G0K58_10200, G0K59_12505, G0K61_08160, G0K65_06450, G0K68_04385, G0K70_15725, G0K72_03355, G0K74_12235, G0K75_06340, G0K78_16920, G0K80_12825, G0K83_04965, G0K85_10130, G0L25_16420, G0L31_14425, G0L32_08690, G0L34_08105, G0L35_20795, G0L36_14945, G0L37_09110, G0L38_11490, G0L40_21035, G0L42_16900, G0L48_07660, G0L49_02470, G0L51_19890, G0L52_20660, G0L55_18750, G0L67_13070, G0L68_20065, G0L70_07980, G0L73_13585, G0L76_17550, G0L77_11200, G0L83_10285, G0L88_19875, G0L93_18390, G0L96_20235, G0L98_18225, G0M00_19570, G0M21_14965, G0M30_17360, G0M33_16950, G0M35_12335, G0M36_18250, G0N45_04380, G0N48_08260, G0N51_11665, G0N53_03490, G0N55_07025, G0N57_13470, G0N58_04060, G0N59_10005, G0N60_09080, G0N61_04965, G0N62_04540, G0N64_06650, G0N65_05590, G0N66_21090, G0N67_06670, G0N71_07665, G0N75_10020, G0N78_06135, G0N82_06235, G0N84_07205, G0N85_03490, G0N86_10660, G0N88_07085, G0N89_05685, G0N90_07165, G0N92_11300, G0N94_07575, G0N95_15445, G0N98_09015, G0N99_10120, G0O00_03325, G0O03_06970, G0O10_06195, G0O14_10965, G0O15_13285, G0O18_14145, G0O19_08800, G0O20_17425, G0O22_05125, G0O25_20055, G0O27_07025, G0O31_07570, G0O32_21335, G0O36_21525, G0O39_04960, G0O40_12880, G0O41_07440, G0O43_08505, G0O44_04920, G0O47_08020, G0O52_21675, G0O55_06740, G0O57_07305, G0O58_09440, G0O59_13640, G0O60_08790, G0O63_04375, G0O66_12960, G0O68_06785, G0O70_08215, G0O71_08220, G0O74_07190, G0O75_06905, G0O77_08060, G0O78_07830, G0O80_06955, G0O81_02860, G0O82_09670, G0O84_08215, G0O85_05165, G0O86_09770, G0O87_07360, G0O88_03240, G0O89_05405, G0O92_08325, G0O93_03630, G0O94_12755, G0O97_09015, G0O99_10900, G0P00_14390, G0P01_14665, G0P02_06035, G0P05_12305, G0P06_07745, G0P08_08440, G0P12_12695, G0P13_05070, G0P17_06150, G0P18_07030, G0P19_04865, G0P24_11795, G0P26_08220, G0P28_08290, G0P30_07950, G0P31_10265, G0P36_13335, G0P37_11525, G0P41_13560, G0P44_12170, G0P45_14285, G0P48_07355, G0P49_11185, G0P52_05035, G0P53_09245, G0P56_09400, G0P57_08220, G0P58_04380, G0P63_13655, G0P65_04270, G0P67_09515, G0P68_15025, G0P69_13380, G0P73_11960, G0P75_19470, G0P76_20900, G1O10_07355, G1P61_07755, G1P78_03080, G1P83_03095, G2203_07390, G2212_08770, G2221_13825, G2290_12030, G2793_12950, G2918_12910, G2951_05600, G3221_002461, G3230_003350, G3231_003124, G3247_001587, G3248_002520, G3263_002773, G3270_002858, G3275_000607, G3312_001215, G3336_001483, G3357_001539, G3369_002117, G3433_003279, G3460_000048, G3464_003259, G3A35_05400, G3V06_004273, G3V14_002992, G3V17_003950, G3V21_001420, G3V56_000436, G3V57_002645, G3X03_004111, G4189_000938, G4190_003975, G4192_004415, G4198_002583, G4201_001978, G4202_001352, G4A01_001700, G4A83_001807, G4A85_000671, G4A87_001005, G4B68_003747, G4B72_003627, G4B74_000558, G4C74_000608, G4D32_004267, G4D46_004008, G4F88_00370, G4F89_00370, G4F91_00370, G4F92_00370, G4G47_002570, G4G67_002555, G4G68_003571, G4G76_003775, G4G79_002547, G4G97_004277, G4H00_000670, G4H04_002753, G4H07_003539, G4H08_003660, G4H18_000608, G4H21_000608, G4H24_000607, G4H63_002557, G4I66_002831, G4J07_001603, G4J08_001574, G4J11_002933, G4J12_003190, G4J18_004388, G4J20_002959, G4J37_003102, G4J39_003166, G4J41_002973, G4J45_002325, G4J90_001589, G4K02_003670, G4K03_001902, G4O54_004300, G4O56_001447, G4O59_004199, G4O60_004410, G4O67_003632, G4O69_004091, G4P29_002967, G4P83_001728, G4P85_000670, G4P89_003632, G4P91_003586, G4P93_003012, G4Q12_001802, G4Q28_000607, G4Q31_000605, G4Q50_002019, G4Q52_001653, G4Q59_002683, G4Q60_000670, G4Q63_002117, G4Q67_003536, G4Q94_003028, G4R01_000669, G4R02_003778, G4R15_003726, G4R16_000614, G4W73_000432, G4W86_003908, G4W87_000607, G4W88_000607, G4W91_000048, G4Y10_003178, G9269_000711, G9302_000670, G9304_003120, G9305_002536, G9309_003364, G9313_000670, G9314_003368, G9367_001351, G9381_002972, G9C24_000259, G9C41_004198, G9C46_002377, G9C47_004436, G9C49_004027, G9C57_000605, G9C64_003813, G9G03_004136, G9G04_002988, G9G34_001906, G9G36_003863, G9G45_002336, G9G50_002760, G9G62_002931, G9W19_002475, G9W28_001548, G9W45_002746, G9W52_002669, G9W63_002107, G9W65_000605, G9W79_002017, G9W95_000608, G9W96_003645, G9X40_002052, GB021_11435, GB040_06400, GB076_10055, GB106_05325, GB114_07815, GB120_04950, GB122_13355, GB139_06265, GB171_03525, GB209_07450, GB221_07260, GB238_15175, GB280_05035, GB321_06910, GB339_12600, GB342_04485, GB368_11605, GB416_12110, GB459_13610, GB466_11405, GB505_11285, GB551_03595, GB645_19215, GBS58_05415, GBW03_18930, GBW44_14320, GBW52_03920, GBW76_13155, GBX20_14340, GBX55_07035, GBX64_03350, GBY13_10615, GBY23_14735, GBY73_05465, GBZ51_19350, GCH31_10010, GCQ81_08735, GCZ80_14565, GEZ01_02385, GJE27_05045, GJE28_03920, GNA88_002595, GNA97_002742, GNA99_002309, GNB28_002637, GNB36_000501, GNB86_003979, GNC11_000604, GNC19_004412, GNC45_003965, GNC75_004026, GNC95_004342, GT380_04835, GTH60_03240, GTH62_18910, GTH63_07720, GTH66_07825, GTH67_16665, GTH68_08150, GTH72_22355, GTH73_04965, GTH75_05695, GTH79_13140, GTH81_12785, GTH85_08460, GTH87_08790, GTH91_16020, GTH93_08215, GTH94_05215, GW08_10275, GXC51_04920, GXC56_04920, GXG40_04920, GYI58_10120, GYI62_000613, GYI77_08610, GYJ04_09620, GYJ24_19790, GYJ27_19010, GYJ30_09425, GYJ32_10720, JO10_10940, KP44_05010, LZ63_11700, NCTC13348_05383, NG02_09455, NG06_03180, NG18_09875, NU83_16200, QA89_05780, QD15_00240, R035_07335, RJ78_11910, SE14_03992, Y934_02410, YG50_14220, YR17_12730, Z700_02955, ZB89_00275, ZC54_05665, ZT09_16440, ZT28_05370, ZT74_02580, ZT89_14290, ZU86_20300, ZU92_09900, ZV06_05630, ZV33_02980, ZV34_03345, ZV38_15785, ZV58_14295, ZV70_05935, ZV78_06520, ZW74_10075, ZX03_14710, ZY23_00235, ZY27_13660, ZY40_20350, ZY51_07350, ZZ18_15495, ZZ43_14445, ZZ77_18640, ZZ79_05625
発現宿主: Escherichia coli (大腸菌)
参照: UniProt: A0A0D6I3R5, L-seryl-tRNASec selenium transferase
#2: 化合物
ChemComp-DMS / DIMETHYL SULFOXIDE / 2-チアプロパン2-オキシド / ジメチルスルホキシド


分子量: 78.133 Da / 分子数: 6 / 由来タイプ: 合成 / 式: C2H6OS / コメント: DMSO, 沈殿剤*YM
#3: 化合物
ChemComp-CA / CALCIUM ION / カルシウムジカチオン


分子量: 40.078 Da / 分子数: 16 / 由来タイプ: 合成 / 式: Ca
#4: 水 ChemComp-HOH / water / 水


分子量: 18.015 Da / 分子数: 150 / 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N

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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

結晶マシュー密度: 3.19 Å3/Da / 溶媒含有率: 61.43 %
結晶化温度: 293 K / 手法: 蒸気拡散法, ハンギングドロップ法 / pH: 8.5
詳細: 0.1 M Tris-HCl, pH 8.5, 0.4 M CaCl2, 11% PEG 4000, 8% glycerol

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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: APS / ビームライン: 22-ID / 波長: 1 Å
検出器タイプ: DECTRIS EIGER X 16M / 検出器: PIXEL / 日付: 2019年8月15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: 2.58→60.37 Å / Num. obs: 48940 / % possible obs: 94.6 % / 冗長度: 14.6 % / Biso Wilson estimate: 78.59 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 18.1
反射 シェル解像度: 2.58→2.676 Å / Num. unique obs: 8157 / CC1/2: 0.629

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解析

ソフトウェア
名称バージョン分類
PHENIX1.19_4092精密化
XDSデータ削減
Aimlessデータスケーリング
PHASER位相決定
Cootモデル構築
精密化構造決定の手法: 分子置換
開始モデル: 7LC0

7lc0


解像度: 2.58→60.37 Å / SU ML: 0.3009 / 交差検証法: FREE R-VALUE / σ(F): 1.33 / 位相誤差: 30.2233
立体化学のターゲット値: GeoStd + Monomer Library + CDL v1.2
Rfactor反射数%反射
Rfree0.2287 2000 4.09 %
Rwork0.1926 46915 -
obs0.1941 48915 75.69 %
溶媒の処理減衰半径: 0.9 Å / VDWプローブ半径: 1.11 Å / 溶媒モデル: FLAT BULK SOLVENT MODEL
原子変位パラメータBiso mean: 87.59 Å2
精密化ステップサイクル: LAST / 解像度: 2.58→60.37 Å
タンパク質核酸リガンド溶媒全体
原子数11096 0 40 155 11291
拘束条件
Refine-IDタイプDev ideal数
X-RAY DIFFRACTIONf_bond_d0.002211310
X-RAY DIFFRACTIONf_angle_d0.516515340
X-RAY DIFFRACTIONf_chiral_restr0.04241767
X-RAY DIFFRACTIONf_plane_restr0.00281991
X-RAY DIFFRACTIONf_dihedral_angle_d11.93324068
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDタイプRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS1.10037416691
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS1.38806225622
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS1.49918698344
LS精密化 シェル
解像度 (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.58-2.650.2630.407882X-RAY DIFFRACTION1.87
2.65-2.720.2291160.3646361X-RAY DIFFRACTION8.3
2.72-2.80.4439340.3688797X-RAY DIFFRACTION18.26
2.8-2.890.361920.33022166X-RAY DIFFRACTION49.7
2.89-2.990.33391520.32863558X-RAY DIFFRACTION81.4
2.99-3.110.35851780.30994178X-RAY DIFFRACTION96.03
3.11-3.250.31451880.28554405X-RAY DIFFRACTION100
3.26-3.430.3091870.274395X-RAY DIFFRACTION99.98
3.43-3.640.2951880.21564402X-RAY DIFFRACTION100
3.64-3.920.21861880.18014419X-RAY DIFFRACTION99.93
3.92-4.320.211900.17024455X-RAY DIFFRACTION99.98
4.32-4.940.20311890.14584458X-RAY DIFFRACTION99.98
4.94-6.220.1931940.18214522X-RAY DIFFRACTION100
6.22-60.370.18342010.15814717X-RAY DIFFRACTION99.55
精密化 TLS

手法: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.49118196102-0.281402563647-0.3177960874581.56050789974-0.1647618348390.4619256352420.1647138869020.573434008535-0.00477825893739-0.346157459891-0.0104128154201-0.07481650591150.189325646304-0.0475146793952-0.08807376645630.4390464706940.05457601939510.1629144109380.5952355874440.1774702068570.37066615536713.275082378550.11317174319.61375681902
22.186826477261.394749541110.2455751923012.254732004261.059610635772.314343330570.1495949290840.1920410938930.607804210619-0.480346924147-0.172758568325-0.248768452067-0.239372578943-0.00626701879327-0.09253630242430.3332076005660.0924877434510.3338095449380.5835781686580.2670916809540.57365694520623.432681897458.657431704816.4256520149
31.49076504083-2.46769208995-0.1365190723576.78055856074-0.5051987736171.44972628269-0.113880699985-0.0007014930809360.329321554444-0.08255713673210.308963597812-0.216973493601-0.184808999693-0.00189888101413-0.1782044925920.584188294158-0.0001592581239940.002501920799740.7993317539060.2755467413280.490325189601-4.3329802391371.85472417694.57931300255
40.4250897241380.2857093516630.727135318360.1787728088650.4620132387711.175682764660.294679253698-0.256322111598-0.4707843728890.0202056920945-0.02899687927050.1890290156290.779502239429-0.371382673864-0.1156891135181.62169857944-0.214739339013-0.2574268508540.2398225370840.1313843227130.7109058373422.9367629097-9.438267941144.9851023494
52.54113358937-0.23133445999-1.10078494082.961050959420.3586733894352.6274099992-0.06321078400070.08720678972250.1250461247830.2228870158250.306080751891-0.3176843621670.5438800027710.424883875334-0.2202658262470.681688769280.107366062507-0.03223861195280.331556355727-0.04576141545390.28604080019239.125432123812.691524790840.0577211017
62.85904334773-1.974631356481.207473142221.63331581287-1.38515240894.378361413570.2975022847760.280632945590.3532091987860.123040510923-0.211612112250.163623122699-0.254876414911-0.512802674364-0.0843319030310.63648440439-0.0008966018079270.08177287718220.3760737015780.08392068656750.49269751185928.46408690523.029351001331.3817799974
71.27825583888-0.825323536099-0.1110590898792.96694192352-0.9496632518791.935750392140.2459212662630.415231701184-0.0332633963114-0.714961457829-0.1619833167840.07632248498650.9698453683420.388029012854-0.08516335603280.8312912755150.192652799198-0.01806962887890.412180414424-0.04664631302890.3801526447434.716262443810.19917489832.6472005445
83.659534308161.992446805342.23018262331.14309050811.295989934271.748870563150.002878494484290.803605165052-0.427912805823-0.3240038143420.2353413202870.2833279027391.02860947228-0.00556857109089-0.03031300050621.969927474120.0147302302218-0.3268791512430.763523653705-0.1257844664370.76693861547824.8711175501-11.933164381231.4302793897
94.05019328797-0.529802529414-1.910220165571.727077753091.713360037843.193459872290.5539868560950.632081714992-0.03522039219560.086980839805-0.178158579965-0.08545383372930.155387335215-0.630508687548-0.2823228075611.65638271689-0.160000033116-0.4617557777770.7610233980190.02398600609290.7476146643794.39424338554-7.7254936120428.9926351479
101.43295409748-0.2772408994110.9522544588710.220097157290.2464118035241.72133528903-0.1130374995310.3832210508030.9380103443940.157613460555-0.257999862780.0356479926911-1.102947897030.3221033245790.4199456424331.03372448902-0.00390330048421-0.001539453440690.514777648640.1510898574751.5408348344830.260514192101.05509770440.4920201342
111.27443534114-0.132035206974-0.2004195138980.7142782776050.1236008524561.92479566999-0.0924931523685-0.4474211157790.3242032531110.2197181332940.144254842630.119000285717-0.111353566337-0.561635840640.003875671902650.1715789749740.1285557374320.2736811276910.551976386979-0.04714738544841.013306440818.336685249278.91671177352.3623242261
123.11005268711-0.4788043235120.283744786781.558903109590.05912780460032.445866327720.1057816828450.4302902885280.061907102277-0.3815622151310.1071037361170.08748690942990.0634414133312-0.19201276165-0.0006493957984120.1271331190030.04268581749750.319484859410.637041931930.04080725054740.88271592020415.936385487568.51762310538.7908620655
132.598745293981.171934787210.7552856618611.193416292271.359518971652.57040504979-0.410560862227-0.14015648560.558192030099-0.597229589612-0.07690127921830.284868225745-0.873154912403-0.731284759212-0.1549412824950.4102589489850.2368965853460.1916718893870.626780905704-0.06713213803491.173553490614.561971577884.085326664445.6319192881
141.384429175370.06075925781440.6533518940592.1840875488-0.4142056945321.97990747793-0.4363964297540.95797092033-0.2117678442050.1695337793470.02241488925210.35594379313-0.801869732933-0.7605950123710.5099953809471.203824923580.1965631546930.03595082479281.583170484430.0288542700451.4090634490520.1666284975100.28539749716.370608831
153.5362545080.5303409020150.171577051282.74455657768-1.039805582752.770791704650.2424247449290.898961093129-0.0920572526590.279150022183-0.14000196913-0.353694142203-0.136213730043-0.171555673307-0.1751784658270.985450075840.131258316891-0.02189540452211.109809354360.2469794926941.3270699255327.9665033713100.08502486618.8356395131
161.48761793419-0.3146021203840.02915362741471.57681040462-0.3389107285081.946540565280.1910912326020.236362120172-0.104421951378-0.24089496847-0.001019074592640.0965772003810.274307426172-0.342878004833-0.1879609824510.476520252939-0.05109456984710.0652519749880.5870073051750.1040592831080.3919654855854.1616714860340.882109185315.101430538
172.80225574534-0.8586533669480.1865959537053.2914692558-2.00366570943.142703188910.2156102682570.00347952682441-0.3736250512330.0336640768169-0.06258233992950.3676887470050.458582037767-0.0661541242303-0.1888210906350.400733075757-0.06588019668310.04147333169390.3928474175160.07072427505420.442150492955.2369597882532.566060437327.2483400222
182.70571967538-1.41724303772-1.074401464334.989831967091.366162316531.12794684545-0.2397523435480.429941181837-0.938310965775-0.4118646722510.09503188489660.0416533223890.63588939066-0.08447237280360.09796870152621.000459271530.02162510975460.104349668470.751814184166-0.06943494917830.6191203331239.3068295358418.5857668841-1.50124095862
精密化 TLSグループ

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 112 )AA1 - 1121 - 112
22chain 'A' and (resid 113 through 247 )AA113 - 247113 - 247
33chain 'A' and (resid 248 through 369 )AA248 - 369248 - 369
44chain 'B' and (resid 1 through 46 )BE1 - 461 - 46
55chain 'B' and (resid 47 through 112 )BE47 - 11247 - 112
66chain 'B' and (resid 113 through 159 )BE113 - 159113 - 159
77chain 'B' and (resid 160 through 247 )BE160 - 247160 - 247
88chain 'B' and (resid 248 through 282 )BE248 - 282248 - 282
99chain 'B' and (resid 283 through 369 )BE283 - 369283 - 369
1010chain 'C' and (resid 1 through 46 )CG1 - 461 - 46
1111chain 'C' and (resid 47 through 112 )CG47 - 11247 - 112
1212chain 'C' and (resid 113 through 159 )CG113 - 159113 - 159
1313chain 'C' and (resid 160 through 263 )CG160 - 263160 - 263
1414chain 'C' and (resid 264 through 324 )CG264 - 324264 - 324
1515chain 'C' and (resid 325 through 369 )CG325 - 369325 - 369
1616chain 'D' and (resid 1 through 112 )DI1 - 1121 - 112
1717chain 'D' and (resid 113 through 247 )DI113 - 247113 - 247
1818chain 'D' and (resid 248 through 369 )DI248 - 369248 - 369

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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

他の情報も見る