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- PDB-6dli: Crystal structure of glutamate racemase from Thermus thermophilus... -

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Basic information

Entry
Database: PDB / ID: 6dli
TitleCrystal structure of glutamate racemase from Thermus thermophilus in complex with Beta-chloro-D-alanine
ComponentsGlutamate racemase
KeywordsISOMERASE / Thermophile / Racemase / Co-factor independent / BCDA
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape
Similarity search - Function
Glutamate 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 ...Glutamate 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
3-chloro-D-alanine / Glutamate racemase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCooling, G.T. / Vance, N.R. / Spies, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)R01 GM097373 United States
CitationJournal: To be Published
Title: Crystal structure of glutamate racemase from Thermus Thermophilus in complex with Beta-chloro-D-alanine
Authors: Cooling, G.T. / Vance, N.R. / Spies, M.A.
History
DepositionJun 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate racemase
B: Glutamate racemase
C: Glutamate racemase
D: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,60411
Polymers119,8344
Non-polymers7707
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8250 Å2
ΔGint-70 kcal/mol
Surface area36690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.888, 95.605, 179.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutamate racemase


Mass: 29958.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: murI, TTHA1643 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5SHT7, glutamate racemase
#2: Chemical
ChemComp-C2N / 3-chloro-D-alanine / 3-CHLOROALANINATE


Type: D-peptide linking / Mass: 123.538 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H6ClNO2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M HEPES, pH 7.5, 2.0 M ammonium formate / PH range: 8.0-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0721 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: May 14, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0721 Å / Relative weight: 1
ReflectionResolution: 2.7→60.054 Å / Num. obs: 39012 / % possible obs: 99.18 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.098 / Net I/σ(I): 12
Reflection shellResolution: 2.7→2.85 Å

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDS2016-01-11data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5HJ7

5hj7


Resolution: 2.7→60.054 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.48
RfactorNum. reflection% reflection
Rfree0.2445 1859 4.81 %
Rwork0.2094 --
obs0.2111 38654 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→60.054 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7554 0 46 50 7650
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0177772
X-RAY DIFFRACTIONf_angle_d1.78710609
X-RAY DIFFRACTIONf_dihedral_angle_d14.4074586
X-RAY DIFFRACTIONf_chiral_restr0.0961240
X-RAY DIFFRACTIONf_plane_restr0.0141382
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7730.43511530.3872703X-RAY DIFFRACTION96
2.773-2.85460.38631300.34412803X-RAY DIFFRACTION99
2.8546-2.94680.38791260.32192790X-RAY DIFFRACTION100
2.9468-3.05210.32551540.29652806X-RAY DIFFRACTION100
3.0521-3.17430.31191420.28952817X-RAY DIFFRACTION100
3.1743-3.31870.35111390.25812813X-RAY DIFFRACTION100
3.3187-3.49370.27771410.23582812X-RAY DIFFRACTION100
3.4937-3.71250.25751510.21332840X-RAY DIFFRACTION100
3.7125-3.99910.24061460.19282827X-RAY DIFFRACTION100
3.9991-4.40150.20721380.17232845X-RAY DIFFRACTION100
4.4015-5.03810.21131350.16272885X-RAY DIFFRACTION99
5.0381-6.34640.20641380.18762910X-RAY DIFFRACTION100
6.3464-60.06830.17431660.1622944X-RAY DIFFRACTION97

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