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- PDB-2jfz: Crystal structure of Helicobacter pylori glutamate racemase in co... -

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Basic information

Entry
Database: PDB / ID: 2jfz
TitleCrystal structure of Helicobacter pylori glutamate racemase in complex with D-Glutamate and an inhibitor
ComponentsGLUTAMATE RACEMASE
KeywordsISOMERASE / CELL WALL / CELL SHAPE / GLUTAMATE RACEMASE / PEPTIDOGLYCAN SYNTHESIS / PEPTIDOGLYCAN BIOSYNTHESIS
Function / homology
Function and homology information


glutamate racemase / glutamate racemase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / identical protein binding
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
Chem-003 / D-GLUTAMIC ACID / Glutamate racemase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLundqvist, T.
CitationJournal: Nature / Year: 2007
Title: Exploitation of Structural and Regulatory Diversity in Glutamate Racemases
Authors: Lundqvist, T. / Fisher, S.L. / Kern, G. / Folmer, R.H.A. / Xue, Y. / Newton, D.T. / Keating, T.A. / Alm, R.A. / De Jonge, B.L.M.
History
DepositionFeb 6, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GLUTAMATE RACEMASE
B: GLUTAMATE RACEMASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2386
Polymers57,0642
Non-polymers1,1734
Water8,107450
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)61.410, 76.310, 108.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GLUTAMATE RACEMASE


Mass: 28532.193 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9ZLT0, glutamate racemase
#2: Chemical ChemComp-003 / 5-METHYL-7-(2-METHYLPROPYL)-2-(NAPHTHALEN-1-YLMETHYL)-3-PYRIDIN-4-YL-2H-PYRAZOLO[3,4-D]PYRIMIDINE-4,6(5H,7H)-DIONE


Mass: 439.509 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C26H25N5O2
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.1 Å3/Da / Density % sol: 44 %
Crystal growpH: 8.5
Details: PROTEIN FORMULATED AT 10 MG/ML WITH 200 MM AMMONIUM ACETATE PH 7.4, 5 MM D-L GLUTAMATE, 1 MM TCEP AND CRYSTALLISED WITH 100 MM TRIS PH 8, 200 MM AMMONIUM SULFATE, 25% PEG 3350 AND 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→15 Å / Num. obs: 40333 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.86→1.96 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.7 / % possible all: 86.4

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Processing

Software
NameVersionClassification
CNX2000.2refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JFX

2jfx


Resolution: 1.86→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 2020 4.6 %RANDOM
Rwork0.2055 ---
obs-40333 --
Solvent computationBsol: 33.2255 Å2 / ksol: 0.365438 e/Å3
Displacement parametersBiso mean: 21.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.497 Å20 Å20 Å2
2--1.667 Å20 Å2
3----2.164 Å2
Refinement stepCycle: LAST / Resolution: 1.86→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 86 450 4507
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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