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- PDB-5hj7: Glutamate Racemase Mycobacterium tuberculosis (MurI) with bound D... -

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Basic information

Entry
Database: PDB / ID: 5hj7
TitleGlutamate Racemase Mycobacterium tuberculosis (MurI) with bound D-glutamate, 2.3 Angstrom resolution, X-ray diffraction
ComponentsGlutamate racemase
KeywordsISOMERASE / glutamate racemase tuberculosis drug design dimer kinetics
Function / homology
Function and homology information


amino-acid racemase activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / plasma membrane
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
D-GLUTAMIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPoen, S. / Nakatani, Y. / Krause, K.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
University of OtagoDoctoral Scholarship New Zealand
CitationJournal: Biochem. J. / Year: 2016
Title: Exploring the structure of glutamate racemase from Mycobacterium tuberculosis as a template for anti-mycobacterial drug discovery.
Authors: Poen, S. / Nakatani, Y. / Opel-Reading, H.K. / Lasse, M. / Dobson, R.C. / Krause, K.L.
History
DepositionJan 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source / pdbx_struct_oper_list / software
Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)58,0904
Polymers57,7962
Non-polymers2942
Water5,585310
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3480 Å2
ΔGint-4 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.796, 95.796, 61.736
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Glutamate racemase


Mass: 28897.979 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: murI, Rv1338, MTCY02B10.02, MTCY130.23 / Plasmid: pET-28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P9WPW9, glutamate racemase
#2: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 310 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50 % / Description: needle shape
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5 / Details: 20% PEG 10,000, 0.1 M HEPES / PH range: 7.5

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Data collection

DiffractionMean temperature: 93 K / Ambient temp details: cryocooling stream
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→42.8 Å / Num. obs: 24018 / % possible obs: 95.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 5 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata scaling
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→42.8 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 19.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 1220 5.08 %Random selection
Rwork0.1541 ---
obs0.1569 24014 95.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3824 0 20 310 4154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073906
X-RAY DIFFRACTIONf_angle_d0.8675330
X-RAY DIFFRACTIONf_dihedral_angle_d14.3532360
X-RAY DIFFRACTIONf_chiral_restr0.053644
X-RAY DIFFRACTIONf_plane_restr0.006706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.23381290.16812434X-RAY DIFFRACTION93
2.3921-2.50090.24361140.17312443X-RAY DIFFRACTION93
2.5009-2.63280.24531310.17232465X-RAY DIFFRACTION94
2.6328-2.79770.28151250.17052509X-RAY DIFFRACTION95
2.7977-3.01370.20711450.16892517X-RAY DIFFRACTION96
3.0137-3.31680.24861420.17012539X-RAY DIFFRACTION97
3.3168-3.79650.18781490.14052590X-RAY DIFFRACTION98
3.7965-4.78220.15621480.12662598X-RAY DIFFRACTION98
4.7822-42.84870.17661370.14632699X-RAY DIFFRACTION99

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