3IST

Crystal structure of glutamate racemase from Listeria monocytogenes in complex with succinic acid

Structural Biology Knowledgebase: 3IST SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.171

Literature

Macromolecules
Sequence Display for 3IST

Classification: ISOMERASE

Total Structure Weight: 59898.09

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate racemase A, B 269 Listeria monocytogenes EC#: 5.1.1.3 IUBMB
Gene Name(s): murI racE lmo1237
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SIN
Query on SIN

A, B SUCCINIC ACID
C4 H6 O4
KDYFGRWQOYBRFD-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
MSE
Query on MSE
A, B L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 66.42 α = 90.00
b = 66.42 β = 90.00
c = 258.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-27
  • Released Date: 2009-09-22
  • Deposition author(s): Majorek, K.A., Chruszcz, M., Skarina, T., Onopriyenko, O., Stam, J., Anderson, W.F., Savchenko, A., Bujnicki, J.M., Minor, W., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor