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- PDB-3s81: Crystal Structure of Putative Aspartate Racemase from Salmonella ... -

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Basic information

Entry
Database: PDB / ID: 3s81
TitleCrystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium
ComponentsPutative aspartate racemase
KeywordsISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta fold / racemase / cytosol
Function / homology
Function and homology information


amino-acid racemase activity / metal ion binding
Similarity search - Function
Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / Rossmann fold - #1860 / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase / Rossmann fold ...Aspartate racemase / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Asp/Glu racemase, active site 2 / Aspartate and glutamate racemases signature 2. / 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
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.796 Å
AuthorsMaltseva, N. / Kim, Y. / Kwon, K. / Zhang, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal Structure of Putative Aspartate Racemase from Salmonella Typhimurium
Authors: Maltseva, N. / Kim, Y. / Kwon, K. / Zhang, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 racemase
B: Putative aspartate racemase
C: Putative aspartate racemase
D: Putative aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,63619
Polymers116,4984
Non-polymers1,13815
Water11,908661
1
A: Putative aspartate racemase
B: Putative aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,83610
Polymers58,2492
Non-polymers5878
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-135 kcal/mol
Surface area18670 Å2
MethodPISA
2
C: Putative aspartate racemase
D: Putative aspartate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8009
Polymers58,2492
Non-polymers5517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-122 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.154, 84.154, 114.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Putative aspartate racemase


Mass: 29124.520 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: STM4510 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8ZJZ9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 661 / Source method: isolated from a natural source / Formula: H2O

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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: 2.01 Å3/Da / Density % sol: 38.82 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1M ammonium sulfate, 0.1M HEPES pH7.0, 0.5% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 24, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 84553 / Num. obs: 84553 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 23.3 Å2 / Rsym value: 0.098 / Net I/σ(I): 8
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 4236 / Rsym value: 0.732 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 3S7Z

3s7z


Resolution: 1.796→45.038 Å / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.49 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.169 4217 4.99 %random
Rwork0.14 ---
all0.143 84513 --
obs0.143 84513 99.82 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.258 Å2 / ksol: 0.384 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.088 Å2-0 Å2-0 Å2
2--4.088 Å2-0 Å2
3----8.176 Å2
Refinement stepCycle: LAST / Resolution: 1.796→45.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7159 0 55 661 7875
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067413
X-RAY DIFFRACTIONf_angle_d1.17610106
X-RAY DIFFRACTIONf_dihedral_angle_d12.3912722
X-RAY DIFFRACTIONf_chiral_restr0.0751174
X-RAY DIFFRACTIONf_plane_restr0.0061294
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7958-1.82680.25032270.2413900412793
1.8268-1.860.24611940.22773954414895
1.86-1.89570.2181920.21414124431696
1.8957-1.93440.21931990.21364008420795
1.9344-1.97650.21672000.19624047424795
1.9765-2.02250.20371920.19544069426195
2.0225-2.0730.21052060.19093985419195
2.073-2.12910.20552160.18394023423995
2.1291-2.19170.19421900.18054035422596
2.1917-2.26240.18352220.16864047426995
2.2624-2.34330.20972120.16324040423295
2.3433-2.4370.16612160.15734001421795
2.437-2.54790.19562090.16024048425795
2.5479-2.68220.19311940.15474032422695
2.6822-2.85010.18822170.14753998421595
2.8501-3.070.17642380.14113968420694
3.07-3.37860.16382360.12124049428594
3.3786-3.86660.14962430.10453954419794
3.8666-4.86840.1242100.08883995420594
4.8684-30.75090.13542040.1144012421695
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)
10.58510.216-0.06731.30930.13342.4839-0.0304-0.0290.01270.0049-0.0257-0.0757-0.10020.09410.05210.1211-0.00840.00620.15560.02620.180326.938728.58588.4166
21.1378-0.13540.34040.408-0.2572.1588-0.00440.0119-0.0526-0.0624-0.0161-0.00910.0504-0.06070.01330.1887-0.02370.04370.1488-0.01730.21127.91615.4247-7.7347
30.5892-0.3174-0.07941.207-0.41012.0674-0.03860.0451-0.0445-0.00520.01730.0352-0.0411-0.06850.01550.1344-0.00690.00930.201-0.04420.2003-24.728825.238511.3528
41.43940.2230.00730.53770.19192.4698-0.0419-0.0067-0.07440.0329-0.0144-0.05060.02260.110.0510.14620.02140.02490.13660.01270.1863-3.920715.209927.3581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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