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- PDB-5hra: Crystal structure of an aspartate/glutamate racemase in complex w... -

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Basic information

Entry
Database: PDB / ID: 5hra
TitleCrystal structure of an aspartate/glutamate racemase in complex with D-aspartate
Componentsaspartate/glutamate racemase
KeywordsISOMERASE / Aspartate/glutamate racemase / PLP-independent racemase / Racemization mechanism
Function / homologyRossmann fold - #1860 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / D-ASPARTIC ACID / :
Function and homology information
Biological speciesEscherichia coli O157:H7 str. SS52 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.597 Å
AuthorsLiu, X. / Gao, F. / Ma, Y. / Liu, S. / Cui, Y. / Yuan, Z. / Kang, X.
CitationJournal: Febs Lett. / Year: 2016
Title: Crystal structure and molecular mechanism of an aspartate/glutamate racemase from Escherichia coli O157
Authors: Liu, X. / Gao, F. / Ma, Y. / Liu, S. / Cui, Y. / Yuan, Z. / Kang, X.
History
DepositionJan 23, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 18, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: aspartate/glutamate racemase
B: aspartate/glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2484
Polymers51,9812
Non-polymers2662
Water7,855436
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-12 kcal/mol
Surface area17200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.938, 48.248, 116.289
Angle α, β, γ (deg.)90.00, 92.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein aspartate/glutamate racemase


Mass: 25990.686 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 str. SS52 (bacteria)
Strain: SS52 / Gene: ygeA, SS52_3985 / Plasmid: pET-21b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: A0A0F6FBL7
#2: Chemical ChemComp-DAS / D-ASPARTIC ACID


Type: D-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H7NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 2.53 Å3/Da / Density % sol: 51.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 9.5
Details: 1.0 M sodium citrate, 0.1 M CHES, 3.0% D (+)-Sucrose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.989 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.597→32.61 Å / Num. obs: 66927 / % possible obs: 96 % / Redundancy: 2.9 % / Net I/σ(I): 16.12
Reflection shellResolution: 1.597→1.654 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2090: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HQT

5hqt


Resolution: 1.597→32.61 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.86
RfactorNum. reflection% reflection
Rfree0.2498 1994 2.98 %
Rwork0.2332 --
obs0.2337 66801 96.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.597→32.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3592 0 18 436 4046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093674
X-RAY DIFFRACTIONf_angle_d1.2944966
X-RAY DIFFRACTIONf_dihedral_angle_d19.3341338
X-RAY DIFFRACTIONf_chiral_restr0.064566
X-RAY DIFFRACTIONf_plane_restr0.005648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5967-1.63660.33811270.30074032X-RAY DIFFRACTION85
1.6366-1.68090.31931530.28654692X-RAY DIFFRACTION98
1.6809-1.73030.28381360.28644732X-RAY DIFFRACTION99
1.7303-1.78620.30671480.27334675X-RAY DIFFRACTION98
1.7862-1.850.30651430.27594691X-RAY DIFFRACTION98
1.85-1.92410.30221400.25944728X-RAY DIFFRACTION99
1.9241-2.01160.25311540.2414710X-RAY DIFFRACTION99
2.0116-2.11770.28331450.23864706X-RAY DIFFRACTION99
2.1177-2.25030.27511430.22964762X-RAY DIFFRACTION99
2.2503-2.4240.24851420.22464681X-RAY DIFFRACTION98
2.424-2.66790.22231450.23084734X-RAY DIFFRACTION98
2.6679-3.05370.25211430.23184704X-RAY DIFFRACTION97
3.0537-3.84650.2121360.21424403X-RAY DIFFRACTION91
3.8465-33.62880.22651390.21484557X-RAY DIFFRACTION91

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