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- PDB-5ell: Crystal structure of L-aspartate/glutamate-specific racemase from... -

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Basic information

Entry
Database: PDB / ID: 5ell
TitleCrystal structure of L-aspartate/glutamate-specific racemase from Escherichia coli
ComponentsAsp/Glu_racemase family protein
KeywordsISOMERASE / Asp/Glu racemase / L-form specific racemase / amino acid enantiomers
Function / homology
Function and homology information


aspartate racemase activity / aspartate racemase / amino-acid racemase activity / amino-acid racemase / glutamate racemase / glutamate racemase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / identical protein 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
L-aspartate/glutamate-specific racemase / Racemase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsAhn, J.W. / Chang, J.H. / Kim, K.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Korea, Republic Of
CitationJournal: Febs Lett. / Year: 2015
Title: Structural basis for an atypical active site of an l-aspartate/glutamate-specific racemase from Escherichia coli
Authors: Ahn, J.W. / Chang, J.H. / Kim, K.J.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 13, 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: Asp/Glu_racemase family protein
B: Asp/Glu_racemase family protein


Theoretical massNumber of molelcules
Total (without water)52,8102
Polymers52,8102
Non-polymers00
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint-11 kcal/mol
Surface area19400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.172, 147.859, 82.182
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

21A-471-

HOH

31A-473-

HOH

41A-543-

HOH

51A-622-

HOH

61B-467-

HOH

71B-541-

HOH

81B-564-

HOH

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Components

#1: Protein Asp/Glu_racemase family protein / Aspartate racemase / Putative racemase / Putative resistance proteins / Racemase / Strain O157 ...Aspartate racemase / Putative racemase / Putative resistance proteins / Racemase / Strain O157 SvETEC scaffold16.1 / whole genome shotgun sequence


Mass: 26405.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET30a(+) / Production host: Escherichia coli (E. coli)
References: UniProt: C3SWD2, UniProt: A0A140N890*PLUS, aspartate racemase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.3 M ammonium nitrate, 14~16% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 46553 / % possible obs: 96.3 % / Redundancy: 4.8 % / Net I/σ(I): 23.53
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 3.44 / % possible all: 90.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JFL

1jfl


Resolution: 1.801→25.687 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2016 2277 5.08 %
Rwork0.164 --
obs0.166 44813 96.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.801→25.687 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 0 616 4219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073663
X-RAY DIFFRACTIONf_angle_d0.954952
X-RAY DIFFRACTIONf_dihedral_angle_d12.791334
X-RAY DIFFRACTIONf_chiral_restr0.039563
X-RAY DIFFRACTIONf_plane_restr0.004644
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.801-1.84020.27751150.25452425X-RAY DIFFRACTION88
1.8402-1.8830.27741360.23142509X-RAY DIFFRACTION92
1.883-1.930.24261420.2162499X-RAY DIFFRACTION92
1.93-1.98220.21961350.1952578X-RAY DIFFRACTION95
1.9822-2.04050.22721330.18652622X-RAY DIFFRACTION95
2.0405-2.10630.23991360.17612638X-RAY DIFFRACTION95
2.1063-2.18160.22921320.16582654X-RAY DIFFRACTION97
2.1816-2.26890.20191220.15942695X-RAY DIFFRACTION97
2.2689-2.37210.2191560.15442684X-RAY DIFFRACTION98
2.3721-2.4970.19471440.15592672X-RAY DIFFRACTION98
2.497-2.65330.18321520.14542689X-RAY DIFFRACTION97
2.6533-2.8580.20731390.15352722X-RAY DIFFRACTION99
2.858-3.14510.18141360.15132758X-RAY DIFFRACTION99
3.1451-3.59910.18211540.1422750X-RAY DIFFRACTION99
3.5991-4.53050.16461700.12942781X-RAY DIFFRACTION99
4.5305-25.68990.20341750.18652860X-RAY DIFFRACTION99

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