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- PDB-3ojc: Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3ojc
TitleCrystal structure of a putative Asp/Glu Racemase from Yersinia pestis
ComponentsPutative aspartate/glutamate racemase
KeywordsISOMERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha beta / 3-layer(aba) sandwich / Rossmann fold / Asp/Glu/Hydantoin racemase family
Function / homology
Function and homology information


aspartate racemase / amino-acid racemase activity / metal ion binding
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Aspartate/glutamate racemase / Aspartate/glutamate racemase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsAnderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis
Authors: Anderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aspartate/glutamate racemase
B: Putative aspartate/glutamate racemase
C: Putative aspartate/glutamate racemase
D: Putative aspartate/glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,99828
Polymers102,4744
Non-polymers2,52424
Water13,385743
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative aspartate/glutamate racemase
C: Putative aspartate/glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,30313
Polymers51,2372
Non-polymers1,06611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-22 kcal/mol
Surface area20050 Å2
MethodPISA
3
B: Putative aspartate/glutamate racemase
D: Putative aspartate/glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,69515
Polymers51,2372
Non-polymers1,45813
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-9 kcal/mol
Surface area20100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.52, 95.41, 142.62
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative aspartate/glutamate racemase


Mass: 25618.457 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: racX, YPO2758, YP_2405 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q74SZ5, UniProt: A0A2S9PI63*PLUS
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 743 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 200mM calcium acetate, 20% PEG 3350, 2% 1,6-hexanediol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2010 / Details: beryllium lens
RadiationMonochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 92148 / Num. obs: 92056 / % possible obs: 99.9 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.083 / Χ2: 1.002 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.75-1.816.40.598390400.97799.9
1.81-1.897.40.4564.891191.016100
1.89-1.977.40.336.391371.029100
1.97-2.077.40.2219.491390.997100
2.07-2.27.50.15113.891131.007100
2.2-2.387.40.12116.392090.99100
2.38-2.617.40.0882391541.003100
2.61-2.997.40.0726.692541.004100
2.99-3.777.30.06624.79300199.9
3.77-506.90.04532.495910.98999.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
BLU-MAXdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→38.77 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 1.44 / σ(I): 3 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2015 4595 5 %random
Rwork0.1699 ---
all0.172 92150 --
obs0.1715 91929 99.76 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.687 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 159.73 Å2 / Biso mean: 26.783 Å2 / Biso min: 6.51 Å2
Baniso -1Baniso -2Baniso -3
1--2.5222 Å20 Å2-0 Å2
2--5.7664 Å20 Å2
3----3.2443 Å2
Refinement stepCycle: LAST / Resolution: 1.75→38.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7072 0 164 743 7979
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077417
X-RAY DIFFRACTIONf_angle_d1.03910000
X-RAY DIFFRACTIONf_chiral_restr0.0771163
X-RAY DIFFRACTIONf_plane_restr0.0041267
X-RAY DIFFRACTIONf_dihedral_angle_d13.042776
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.7499-1.81250.2484480.219785118959895999
1.8125-1.88510.24244560.1902865791139113100
1.8851-1.97080.23264560.180586699125912599.9
1.9708-2.07470.20114580.1588869991579157100
2.0747-2.20470.19154560.1503866391199119100
2.2047-2.37490.19294600.155787349194919499.9
2.3749-2.61390.19144570.1568869791549154100
2.6139-2.9920.19144640.167879892629262100
2.992-3.76910.19084640.166588369300930099.9
3.7691-38.77590.20454760.179690709546954699
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)
11.40340.27640.42261.597-0.36390.7923-0.00120.0225-0.0332-0.04190.003-0.04090.0785-0.01650.00190.0973-0.0102-0.00380.09710.00660.064543.515757.920487.9183
22.0310.1902-1.87580.72680.4993.62560.0683-0.23380.27070.16360.1010.2997-0.12160.1645-0.16060.15090.03010.05040.1539-0.00350.213830.4869.743894.325
31.06971.0107-0.46962.2262-0.79011.07480.08090.06430.0780.1961-0.05180.2358-0.069-0.0598-0.02870.093-0.00120.00750.1015-0.01420.113229.113753.668791.1481
41.6680.977-1.03321.30540.39941.99110.0572-0.40250.30110.1783-0.16410.2754-0.00910.03290.08220.1356-0.02760.03420.1033-0.04260.166232.601349.9524109.1829
51.54830.1111-0.20441.55230.47491.4556-0.032-0.1009-0.15270.0841-0.0469-0.02240.2270.15970.0590.1258-0.00240.01370.0694-0.01030.116936.748243.1538100.7637
61.0418-0.7046-0.17970.79260.23931.4374-0.0304-0.0024-0.09180.0978-0.00690.11460.1187-0.17570.04680.1171-0.0192-0.00220.1113-0.00290.113846.345666.3719123.9581
71.8569-0.4968-0.32321.74570.53980.2731-0.1123-0.4578-0.23310.49940.0690.1640.26020.15680.05220.2406-0.00630.03230.19790.02730.140448.188364.5488136.2967
80.9421-0.68020.03250.90660.50731.0256-0.1437-0.09890.00590.20080.1598-0.05880.14440.0781-0.00430.09870.0124-0.02320.075-0.02190.037745.89173.0877136.2121
91.28070.1051-0.46811.65550.07671.1182-0.06980.00160.02230.13110.04460.13490.0398-0.03190.03230.0839-0.00650.00160.0943-0.02840.071225.849466.9023131.759
101.8680.8302-0.78731.2904-0.23840.7324-0.11670.12630.008-0.08460.03550.07850.0976-0.10850.07250.0976-0.0210.00230.0962-0.02680.075527.385768.9557123.8179
111.11760.3137-0.18581.4184-0.30610.9864-0.0167-0.0557-0.0184-0.0013-0.0197-0.1062-0.12850.13360.02970.07480.0063-0.0030.1030.01010.091850.272265.687387.5473
121.19370.1205-0.60090.98030.00121.1258-0.08410.2290.0342-0.10520.0562-0.0416-0.01490.05180.01660.0979-0.00050.00220.14590.02690.096453.440371.712276.4687
131.0788-0.5877-0.68830.95470.04890.8905-0.04360.05250.1455-0.07330.0376-0.0489-0.05990.1292-0.00850.1088-0.01610.00410.16160.02770.169972.163172.561280.1928
142.7911-0.6448-0.69950.6051-0.07292.4023-0.1583-0.3639-0.68320.14860.07150.14270.6958-0.14830.11010.22790.00550.02020.16820.07460.270173.846155.81583.2379
151.3365-0.9466-0.4561.34850.570.707-0.1054-0.3251-0.06920.18480.0914-0.00230.06870.17240.01450.14410.0024-0.01470.22090.03860.126267.027968.665990.3661
161.1122-0.7840.41351.31540.13480.388-0.0309-0.1033-0.15250.15490.0620.01180.1023-0.0528-0.02980.1206-0.0182-0.01770.10650.0060.074154.589958.1467126.0305
171.6016-0.9077-0.21880.87530.07931.03460.02980.28860.408-0.1117-0.0107-0.399-0.2099-0.15120.00420.102-0.03330.01310.15030.00680.233567.133570.4846119.3419
182.4233-1.38940.14462.270.27232.83280.026-0.081-0.099-0.11020.0069-0.22440.23560.3179-0.02810.06110.0295-0.01360.06760.00150.054268.445455.8146123.4575
192.145-0.6756-0.12870.85080.13056.39110.17410.572-0.0004-0.1886-0.137-0.10460.79750.0823-0.0320.26710.06070.01910.1809-0.0090.127164.942147.7784105.6799
201.5586-0.4635-0.51770.4795-0.77135.4559-0.103-0.0907-0.4440.10970.08480.04361.26420.10240.03760.34440.0031-0.01460.0980.03320.188461.557746.5228123.197
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:48)A1 - 48
2X-RAY DIFFRACTION2(chain A and resid 49:75)A49 - 75
3X-RAY DIFFRACTION3(chain A and resid 76:120)A76 - 120
4X-RAY DIFFRACTION4(chain A and resid 121:179)A121 - 179
5X-RAY DIFFRACTION5(chain A and resid 180:231)A180 - 231
6X-RAY DIFFRACTION6(chain B and resid 1:28)B1 - 28
7X-RAY DIFFRACTION7(chain B and resid 29:63)B29 - 63
8X-RAY DIFFRACTION8(chain B and resid 64:107)B64 - 107
9X-RAY DIFFRACTION9(chain B and resid 108:180)B108 - 180
10X-RAY DIFFRACTION10(chain B and resid 181:231)B181 - 231
11X-RAY DIFFRACTION11(chain C and resid 1:53)C1 - 53
12X-RAY DIFFRACTION12(chain C and resid 54:112)C54 - 112
13X-RAY DIFFRACTION13(chain C and resid 113:154)C113 - 154
14X-RAY DIFFRACTION14(chain C and resid 155:187)C155 - 187
15X-RAY DIFFRACTION15(chain C and resid 188:231)C188 - 231
16X-RAY DIFFRACTION16(chain D and resid 1:48)D1 - 48
17X-RAY DIFFRACTION17(chain D and resid 49:75)D49 - 75
18X-RAY DIFFRACTION18(chain D and resid 76:117)D76 - 117
19X-RAY DIFFRACTION19(chain D and resid 118:209)D118 - 209
20X-RAY DIFFRACTION20(chain D and resid 210:231)D210 - 231

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