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- PDB-5hqt: Crystal structure of an aspartate/glutamate racemase from Escheri... -

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Basic information

Entry
Database: PDB / ID: 5hqt
TitleCrystal structure of an aspartate/glutamate racemase from Escherichia coli O157
Componentsaspartate/glutamate racemase
KeywordsISOMERASE / Aspartate/glutamate racemase / PLP-independent racemase / Racemization mechanism
Function / homologyRossmann fold - #1860 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesEscherichia coli O157:H7 str. SS52 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.598 Å
AuthorsLiu, X. / Gao, F. / Ma, Y. / Liu, S. / Cui, Y. / Yuan, Z. / Kang, X.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Fund31300056 China
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 22, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1982
Polymers25,9911
Non-polymers2071
Water3,585199
1
A: aspartate/glutamate racemase
hetero molecules

A: aspartate/glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3964
Polymers51,9812
Non-polymers4152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3590 Å2
ΔGint-8 kcal/mol
Surface area18020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.985, 46.489, 117.533
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein aspartate/glutamate racemase


Mass: 25990.686 Da / Num. of mol.: 1
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-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.598→50 Å / Num. obs: 34485 / % possible obs: 93 % / Redundancy: 6.2 % / Net I/σ(I): 22.36
Reflection shellResolution: 1.598→1.655 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_2257: ???)refinement
HKL-2000data processing
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OJC

3ojc


Resolution: 1.598→19.991 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 22.65
RfactorNum. reflection% reflection
Rfree0.2211 1928 5.8 %
Rwork0.1827 --
obs0.1849 33261 93.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.598→19.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1821 0 13 199 2033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121878
X-RAY DIFFRACTIONf_angle_d1.162539
X-RAY DIFFRACTIONf_dihedral_angle_d17.3261117
X-RAY DIFFRACTIONf_chiral_restr0.074286
X-RAY DIFFRACTIONf_plane_restr0.007329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5982-1.63810.28231260.25012046X-RAY DIFFRACTION87
1.6381-1.68240.26921420.23362132X-RAY DIFFRACTION92
1.6824-1.73190.28391290.23712221X-RAY DIFFRACTION93
1.7319-1.78770.26661410.21592207X-RAY DIFFRACTION94
1.7877-1.85160.24781380.20732259X-RAY DIFFRACTION95
1.8516-1.92570.23661400.18982259X-RAY DIFFRACTION96
1.9257-2.01320.22461420.17452277X-RAY DIFFRACTION96
2.0132-2.11930.24421350.17912281X-RAY DIFFRACTION96
2.1193-2.25190.22561430.16952278X-RAY DIFFRACTION96
2.2519-2.42550.20831330.17282280X-RAY DIFFRACTION94
2.4255-2.6690.20031380.1832255X-RAY DIFFRACTION93
2.669-3.05410.20331390.17982246X-RAY DIFFRACTION93
3.0541-3.84330.18851330.16442216X-RAY DIFFRACTION90
3.8433-19.99230.22161490.17782376X-RAY DIFFRACTION92

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