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- PDB-5w1q: Crystal structure of alternate isoform of glutamate racemase from... -

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Basic information

Entry
Database: PDB / ID: 5w1q
TitleCrystal structure of alternate isoform of glutamate racemase from Helicobacter pylori bound to D-glutamate
ComponentsGlutamate racemase
KeywordsISOMERASE / racemase / cofactor independent / glutamate
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
D-GLUTAMIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsVance, N.R. / Spies, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM097373 United States
CitationJournal: To Be Published
Title: Crystal structure of alternate isoform of glutamate racemase from Helicobacter pylori bound to D-glutamate
Authors: Vance, N.R. / Spies, M.A.
History
DepositionJun 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1629
Polymers61,4072
Non-polymers7557
Water8,089449
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-23 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.878, 85.555, 105.989
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-550-

HOH

21B-491-

HOH

31B-594-

HOH

41B-636-

HOH

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Components

#1: Protein Glutamate racemase


Mass: 30703.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: murI, OUM_0701 / Production host: Escherichia coli (E. coli) / References: UniProt: K2K6A3, glutamate racemase
#2: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 449 / 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: 2.28 Å3/Da / Density % sol: 46.16 % / Description: cubic
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris, pH 7.5-8.5, 200 mM ammonium acetate, 20-25% PEG3350, 20% glycerol
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.001374 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Jun 4, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.001374 Å / Relative weight: 1
ReflectionResolution: 1.95→61.88 Å / Num. obs: 41793 / % possible obs: 100 % / Redundancy: 6.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.122 / Rrim(I) all: 0.224 / Net I/σ(I): 10.3
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6006 / CC1/2: 0.572 / Rpim(I) all: 0.734 / Rrim(I) all: 1.335 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSVERSION May 1, 2016data reduction
SCALA3.3.22data scaling
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JFY

2jfy


Resolution: 1.95→61.878 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.54
RfactorNum. reflection% reflection
Rfree0.2275 2089 5.01 %
Rwork0.1684 --
obs0.1714 41703 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.95→61.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 50 449 4379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134049
X-RAY DIFFRACTIONf_angle_d1.1095514
X-RAY DIFFRACTIONf_dihedral_angle_d14.3692391
X-RAY DIFFRACTIONf_chiral_restr0.066645
X-RAY DIFFRACTIONf_plane_restr0.008697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.99540.31151350.25422607X-RAY DIFFRACTION100
1.9954-2.04530.24941360.24182597X-RAY DIFFRACTION100
2.0453-2.10060.26371420.22442578X-RAY DIFFRACTION100
2.1006-2.16240.30411230.20192621X-RAY DIFFRACTION99
2.1624-2.23220.24391330.18922605X-RAY DIFFRACTION100
2.2322-2.3120.26961460.19072611X-RAY DIFFRACTION100
2.312-2.40450.24121370.17592615X-RAY DIFFRACTION100
2.4045-2.5140.23511370.16572625X-RAY DIFFRACTION100
2.514-2.64650.22311460.16382590X-RAY DIFFRACTION100
2.6465-2.81230.27041400.15842652X-RAY DIFFRACTION100
2.8123-3.02950.20341480.1622641X-RAY DIFFRACTION100
3.0295-3.33430.20041380.14912648X-RAY DIFFRACTION100
3.3343-3.81670.17071430.13642671X-RAY DIFFRACTION100
3.8167-4.80840.18611270.12712734X-RAY DIFFRACTION100
4.8084-61.90910.24891580.1862819X-RAY DIFFRACTION100

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