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- PDB-8tba: Crystal structure of Helicobacter pylori glutamate racemase bound... -

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Basic information

Entry
Database: PDB / ID: 8tba
TitleCrystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a crystallographic artifact
ComponentsGlutamate racemase
KeywordsISOMERASE / Enzyme / Epimerase / Gyrase / Artifiact
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: 1.65 Å
AuthorsPropp, J. / Spies, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM138471-01 United States
CitationJournal: To Be Published
Title: Crystal structure of Helicobacter pylori glutamate racemase bound to D-glutamate and a likely crystallographic artifact
Authors: Propp, J. / Spies, M.A.
History
DepositionJun 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2024Provider: 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)58,2567
Polymers57,3412
Non-polymers9155
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-10 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.350, 79.868, 114.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Glutamate racemase


Mass: 28670.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: murI / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1W0VMR6
#2: Chemical ChemComp-ZMX / (2M)-N-(1,5-dimethyl-3-oxo-2-phenyl-2,3-dihydro-1H-pyrazol-4-yl)-2-[5-(4-methylphenyl)-1,3-oxazol-2-yl]benzamide


Mass: 464.515 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 10g/l Glutamate Racemase in crystal buffer (0.2M Ammonium Acetate, 5mM D/L-glutamate, 1mM TCEP, pH 7.4) with 10% DMSO and 2.5mM compound (incubated in fridge for 1 week) combined 2:1 with ...Details: 10g/l Glutamate Racemase in crystal buffer (0.2M Ammonium Acetate, 5mM D/L-glutamate, 1mM TCEP, pH 7.4) with 10% DMSO and 2.5mM compound (incubated in fridge for 1 week) combined 2:1 with INDEX G4 (25% PEG3350, 0.2M LiSO4, 0.1M Tris Base) pH 7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.65→79.87 Å / Num. obs: 70675 / % possible obs: 99.8 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.017 / Rrim(I) all: 0.053 / Χ2: 0.89 / Net I/σ(I): 21.7 / Num. measured all: 708160
Reflection shellResolution: 1.65→1.68 Å / % possible obs: 99.5 % / Redundancy: 10.4 % / Rmerge(I) obs: 1.049 / Num. measured all: 35758 / Num. unique obs: 3437 / CC1/2: 0.871 / Rpim(I) all: 0.335 / Rrim(I) all: 1.103 / Χ2: 0.58 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→65.58 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 3587 5.08 %
Rwork0.1869 --
obs0.1883 70586 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→65.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3912 0 0 362 4274
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074005
X-RAY DIFFRACTIONf_angle_d0.8655446
X-RAY DIFFRACTIONf_dihedral_angle_d15.8741428
X-RAY DIFFRACTIONf_chiral_restr0.057626
X-RAY DIFFRACTIONf_plane_restr0.006683
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.670.3111380.30612556X-RAY DIFFRACTION99
1.67-1.690.31611350.28572488X-RAY DIFFRACTION99
1.69-1.720.29131170.27382570X-RAY DIFFRACTION99
1.72-1.740.29221410.26152529X-RAY DIFFRACTION99
1.74-1.770.28071300.25242561X-RAY DIFFRACTION100
1.77-1.80.27911370.23762520X-RAY DIFFRACTION100
1.8-1.830.26951420.25072536X-RAY DIFFRACTION100
1.83-1.870.30741290.24622579X-RAY DIFFRACTION100
1.87-1.90.26581220.23082554X-RAY DIFFRACTION100
1.9-1.940.23241510.222511X-RAY DIFFRACTION99
1.94-1.980.25491460.21412545X-RAY DIFFRACTION100
1.98-2.030.23131370.21222582X-RAY DIFFRACTION100
2.03-2.080.23131570.20652526X-RAY DIFFRACTION100
2.08-2.130.21681230.19832572X-RAY DIFFRACTION100
2.14-2.20.19831360.19492583X-RAY DIFFRACTION100
2.2-2.270.22771520.19532569X-RAY DIFFRACTION100
2.27-2.350.26671380.19812575X-RAY DIFFRACTION100
2.35-2.440.21831380.22570X-RAY DIFFRACTION100
2.44-2.560.25911370.19592594X-RAY DIFFRACTION100
2.56-2.690.23681330.19872578X-RAY DIFFRACTION100
2.69-2.860.23381290.20142612X-RAY DIFFRACTION99
2.86-3.080.26671290.20622612X-RAY DIFFRACTION100
3.08-3.390.21931290.18712627X-RAY DIFFRACTION100
3.39-3.880.2161500.17472617X-RAY DIFFRACTION100
3.88-4.890.16141460.14742675X-RAY DIFFRACTION100
4.89-65.580.17331650.16892758X-RAY DIFFRACTION99

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