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- PDB-8eb3: Crystal structure of glutamate racemase from Helicobacter pylori ... -

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Basic information

Entry
Database: PDB / ID: 8eb3
TitleCrystal structure of glutamate racemase from Helicobacter pylori in complex with a fragment
ComponentsGlutamate racemase
KeywordsISOMERASE / glutamate racemase
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 2 / Asp/Glu racemase, active site 1 / Aspartate and glutamate racemases signature 1. / Aspartate and glutamate racemases signature 2. / Asp/Glu racemase / Asp/Glu/hydantoin racemase / Asp/Glu/Hydantoin racemase
Similarity search - Domain/homology
D-GLUTAMIC ACID / Chem-WFI / Glutamate racemase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCooling, G.T. / Propp, J. / Spies, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)RO1 GM097373 United States
CitationJournal: To Be Published
Title: Crystal structure of glutamate racemase from Helicobacter pylori in complex with a fragment
Authors: Cooling, G.T. / Propp, J. / Spies, M.A.
History
DepositionAug 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release

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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)59,21911
Polymers58,1382
Non-polymers1,0819
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-26 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.002, 95.985, 57.074
Angle α, β, γ (deg.)90.000, 112.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutamate racemase


Mass: 29068.922 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 BL21(DE3) (bacteria) / References: UniProt: K2K6A3, glutamate racemase

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Non-polymers , 6 types, 155 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-WFI / 1-[4-methyl-2-(pyridin-4-yl)-1,3-thiazol-5-yl]methanamine


Mass: 205.279 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H11N3S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.32 Å3/Da / Density % sol: 46.87 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.075 mM Tris pH pH 8.47, 150 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.0721 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Dec 1, 2021
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: 2.2→47.99 Å / Num. obs: 26023 / % possible obs: 97.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 34.64 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.037 / Rrim(I) all: 0.07 / Net I/σ(I): 12.4 / Num. measured all: 85935 / Scaling rejects: 3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.272.70.233571921050.8790.1680.2894.792.1
9.07-47.993.50.03213313810.9970.020.03720.494.1

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W1Q

5w1q


Resolution: 2.2→47.99 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.256 1322 5.1 %
Rwork0.2143 24623 -
obs0.2163 25945 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.89 Å2 / Biso mean: 47.5703 Å2 / Biso min: 22.02 Å2
Refinement stepCycle: final / Resolution: 2.2→47.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3861 0 134 146 4141
Biso mean--49.48 38.39 -
Num. residues----510
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.290.33941460.29792600274693
2.29-2.390.34081170.26562728284597
2.39-2.520.28791600.23982780294099
2.52-2.680.27731650.24882717288298
2.68-2.880.33711540.2452768292298
2.88-3.170.29481520.23642777292998
3.17-3.630.26631540.21632719287397
3.63-4.570.21741260.18252751287796
4.58-47.990.19221480.18342783293197

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