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- PDB-7uj5: Crystal structure of glutamate racemase from Helicobacter pylori ... -

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Basic information

Entry
Database: PDB / ID: 7uj5
TitleCrystal structure of glutamate racemase from Helicobacter pylori in complex with D-glutamate
ComponentsGlutamate racemase
KeywordsISOMERASE / Racemase / Co-factor independent
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 / Glutamate racemase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsCooling, G.T. / 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 D-glutamate
Authors: Cooling, G.T. / Spies, M.A.
History
DepositionMar 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)115,98712
Polymers115,0304
Non-polymers9578
Water17,511972
1
A: Glutamate racemase
B: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9946
Polymers57,5152
Non-polymers4784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-15 kcal/mol
Surface area20820 Å2
MethodPISA
2
C: Glutamate racemase
D: Glutamate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9946
Polymers57,5152
Non-polymers4784
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-15 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.042, 86.335, 107.658
Angle α, β, γ (deg.)90.000, 91.620, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Glutamate racemase


Mass: 28757.562 Da / Num. of mol.: 4
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
#2: Chemical
ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H9NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 972 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 18-32% PEG4000, 200 mM MgSO4, 100 mM Tris pH 8.00

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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 7, 2018
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: 1.75→40.06 Å / Num. obs: 111650 / % possible obs: 97.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 20.78 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.041 / Rrim(I) all: 0.08 / Net I/σ(I): 12.8 / Num. measured all: 409549
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
1.75-1.783.40.7621892855230.6030.4850.9061.598
9.59-40.063.50.02324216940.9990.0140.02733.494

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5W1Q

5w1q


Resolution: 1.75→40.06 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 5543 4.98 %
Rwork0.1787 105745 -
obs0.1807 111288 97.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.25 Å2 / Biso mean: 28.714 Å2 / Biso min: 10.13 Å2
Refinement stepCycle: final / Resolution: 1.75→40.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7866 0 123 972 8961
Biso mean--27.82 31.26 -
Num. residues----1024
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.75-1.770.34711880.2743534372297
1.77-1.790.26061680.24383470363898
1.79-1.810.28691780.22223493367197
1.81-1.840.26671870.22163566375398
1.84-1.860.29161720.24393531370397
1.86-1.890.35691870.30513460364797
1.89-1.910.36671790.33043511369097
1.91-1.940.33411910.30133551374298
1.94-1.970.27161750.23143564373998
1.97-20.23311760.20143570374698
2-2.040.21871930.18533512370598
2.04-2.070.2311970.18793553375099
2.07-2.110.25441620.1843564372699
2.11-2.160.21871920.18683576376898
2.16-2.20.26851700.22593529369997
2.2-2.260.32311700.25283504367498
2.26-2.310.29552100.21893460367096
2.31-2.370.22192040.1763555375999
2.38-2.440.20241920.16233533372598
2.44-2.520.20381860.15533562374898
2.52-2.610.21721970.16353555375298
2.61-2.720.21312090.16413533374298
2.72-2.840.23191590.16913547370697
2.84-2.990.21411850.17473540372597
2.99-3.180.23071910.16593443363496
3.18-3.420.21221590.16613502366195
3.42-3.770.20691840.15473417360194
3.77-4.310.15831770.13583476365395
4.31-5.430.14642010.12043517371896
5.43-40.060.17072040.16143617382197

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