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

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Basic information

Entry
Database: PDB / ID: 5hrc
TitleCrystal structure of an aspartate/glutamate racemase in complex with L-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 / ASPARTIC ACID / :
Function and homology information
Biological speciesEscherichia coli O157:H7 str. SS52 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.765 Å
AuthorsLiu, X. / Gao, F. / Ma, Y. / Liu, S. / Cui, Y. / Yuan, Z. / Kang, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Funds of China31300056 China
Foundation of Hebei Educational committeeYQ2014007 China
Natural Science Foundation of HeBei ProvinceC2014201039 China
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)52,4555
Polymers51,9812
Non-polymers4733
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-8 kcal/mol
Surface area17030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.779, 48.234, 114.784
Angle α, β, γ (deg.)90.00, 95.12, 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-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C4H7NO4
#3: Chemical ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
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: Oct 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.989 Å / Relative weight: 1
ReflectionResolution: 1.765→32.73 Å / Num. obs: 48432 / % possible obs: 91 % / Redundancy: 3.4 % / Net I/σ(I): 20.06
Reflection shellResolution: 1.765→1.828 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HQT

5hqt


Resolution: 1.765→32.73 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2577 2345 5.09 %
Rwork0.2182 --
obs0.2202 46028 91.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.765→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3573 0 31 504 4108
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073660
X-RAY DIFFRACTIONf_angle_d0.8744945
X-RAY DIFFRACTIONf_dihedral_angle_d15.9972184
X-RAY DIFFRACTIONf_chiral_restr0.047564
X-RAY DIFFRACTIONf_plane_restr0.004642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7652-1.80130.34231070.29252322X-RAY DIFFRACTION82
1.8013-1.84040.32071410.26292438X-RAY DIFFRACTION88
1.8404-1.88320.3351530.24242512X-RAY DIFFRACTION90
1.8832-1.93030.27361310.23352528X-RAY DIFFRACTION91
1.9303-1.98250.29791370.22932571X-RAY DIFFRACTION92
1.9825-2.04080.29771570.22872608X-RAY DIFFRACTION93
2.0408-2.10670.26921430.22292624X-RAY DIFFRACTION94
2.1067-2.1820.23421450.21252586X-RAY DIFFRACTION93
2.182-2.26930.25631380.21722649X-RAY DIFFRACTION94
2.2693-2.37260.24761400.21362632X-RAY DIFFRACTION95
2.3726-2.49760.2851280.21812696X-RAY DIFFRACTION94
2.4976-2.6540.23421230.21032681X-RAY DIFFRACTION95
2.654-2.85880.27211490.22612735X-RAY DIFFRACTION97
2.8588-3.14630.23031500.21662718X-RAY DIFFRACTION96
3.1463-3.60110.25611370.2052545X-RAY DIFFRACTION90
3.6011-4.53510.21121160.19112185X-RAY DIFFRACTION77
4.5351-32.73550.24521500.222653X-RAY DIFFRACTION91

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