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

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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 / 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 / Water


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

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.19 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

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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

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