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

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Basic information

Entry
Database: PDB / ID: 8udi
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: 2.1 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: Structure of H. Pylori Glutamate Racemace with a crystallographic artifact
Authors: Propp, J. / Spies, M.A.
History
DepositionSep 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 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)57,6067
Polymers56,8382
Non-polymers7685
Water3,027168
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-40 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.317, 81.969, 113.937
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Glutamate racemase


Mass: 28419.037 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-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: Chemical ChemComp-WAW / N-{[(3S)-2-(3-fluoropyrazin-2-yl)-1,2,3,4-tetrahydroisoquinolin-3-yl]methyl}-1H-indazole-4-carboxamide


Mass: 402.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H19FN6O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.58 Å3/Da / Density % sol: 52.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 4.5g/l HpGR 200mM Ammonium Acetate, 5mM D/L-Glutamate 20% DMSO 2.5mM ligand mixed 2:1 with INDEX G1 8% DMSO 1mM M3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9272 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9272 Å / Relative weight: 1
ReflectionResolution: 2.1→81.97 Å / Num. obs: 34681 / % possible obs: 99.7 % / Redundancy: 5.2 % / Biso Wilson estimate: 42.51 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.02 / Rrim(I) all: 0.047 / Χ2: 0.95 / Net I/σ(I): 22.6 / Num. measured all: 180639
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 99.9 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.523 / Num. measured all: 15389 / Num. unique obs: 2818 / CC1/2: 0.906 / Rpim(I) all: 0.24 / Rrim(I) all: 0.577 / Χ2: 0.76 / Net I/σ(I) obs: 3.9

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→66.54 Å / SU ML: 0.235 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.0366
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 1671 4.83 %
Rwork0.1901 32941 -
obs0.1922 34612 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 47.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→66.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3845 0 52 168 4065
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00763989
X-RAY DIFFRACTIONf_angle_d0.86035423
X-RAY DIFFRACTIONf_chiral_restr0.0548625
X-RAY DIFFRACTIONf_plane_restr0.0069680
X-RAY DIFFRACTIONf_dihedral_angle_d17.55441435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.29581290.2272732X-RAY DIFFRACTION99.79
2.16-2.230.28941530.20452698X-RAY DIFFRACTION99.96
2.23-2.310.27721240.21222701X-RAY DIFFRACTION99.72
2.31-2.40.26621370.20862743X-RAY DIFFRACTION99.72
2.4-2.510.27671300.20552712X-RAY DIFFRACTION99.65
2.51-2.650.28431360.21082727X-RAY DIFFRACTION99.72
2.65-2.810.28641120.22042745X-RAY DIFFRACTION99.83
2.81-3.030.26051520.23642744X-RAY DIFFRACTION99.86
3.03-3.330.27631270.21092753X-RAY DIFFRACTION99.45
3.33-3.820.24631400.19782750X-RAY DIFFRACTION99.07
3.82-4.810.20941590.15572779X-RAY DIFFRACTION99.16
4.81-66.540.17551720.16752857X-RAY DIFFRACTION98.22

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