[English] 日本語
Yorodumi
- PDB-7lce: Structure of D-Glucosaminate-6-phosphate Ammonia-lyase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7lce
TitleStructure of D-Glucosaminate-6-phosphate Ammonia-lyase
ComponentsD-glucosaminate-6-phosphate ammonia lyase
KeywordsLYASE / Aminotransferase fold / D-glucosaminate metabolism
Function / homologyD-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
Function and homology information
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsPhillips, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01-GM137008 United States
CitationJournal: Biochemistry / Year: 2021
Title: 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 ...Title: 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.
Authors: Phillips, R.S. / Ting, S.C. / Anderson, K.
History
DepositionJan 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,48626
Polymers158,3764
Non-polymers1,11022
Water2,702150
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
hetero molecules

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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,97252
Polymers316,7528
Non-polymers2,22044
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Unit cell
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
IDModelComponents
11B-526-

HOH

21C-513-

HOH

31D-544-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
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 domain segments:
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:
IDCodeMatrixVector
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

-
Components

#1: Protein
D-glucosaminate-6-phosphate ammonia lyase / Selenocysteine synthase / Transferase


Mass: 39593.957 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: 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_ ...Gene: 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
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0D6I3R5, L-seryl-tRNASec selenium transferase
#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl, pH 8.5, 0.4 M CaCl2, 11% PEG 4000, 8% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→60.37 Å / Num. obs: 48940 / % possible obs: 94.6 % / Redundancy: 14.6 % / Biso Wilson estimate: 78.59 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 18.1
Reflection shellResolution: 2.58→2.676 Å / Num. unique obs: 8157 / CC1/2: 0.629

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LC0

7lc0


Resolution: 2.58→60.37 Å / SU ML: 0.3009 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.2233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 2000 4.09 %
Rwork0.1926 46915 -
obs0.1941 48915 75.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.59 Å2
Refinement stepCycle: LAST / Resolution: 2.58→60.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11096 0 40 155 11291
Refine LS restraints
Refine-IDTypeDev idealNumber
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-IDTypeRms 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 refinement shell
Resolution (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
Refinement TLS params.

Method: 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
Refinement TLS group

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

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

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more