3TX8

Crystal structure of a succinyl-diaminopimelate desuccinylase (ArgE) from Corynebacterium glutamicum ATCC 13032 at 2.97 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.97 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.238

Literature

Macromolecules
Sequence Display for 3TX8

Classification: HYDROLASE

Total Structure Weight: 40401.61

Macromolecule Entities
Molecule Chains Length Organism Details
Succinyl-diaminopimelate desuccinylase A 369 Corynebacterium glutamicum EC#: 3.5.1.18 IUBMB
Mutation: E4N, ΔL5, K6Q
Gene Name(s): dapE Cgl1109 cg1260
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
PO4
Query on PO4

A PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A 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 L-PEPTIDE LINKING C5 H11 N O2 Se MET

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 82.90 α = 90.00
b = 82.90 β = 90.00
c = 364.17 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-09-22
  • Released Date: 2011-10-26
  • Deposition author(s): Joint Center for Structural Genomics (JCSG), Brunger, A.T., Terwilliger, T.C., Read, R.J., Adams, P.D., Levitt, M., Schroder, G.F.

Revision History

  • Version 1_0: 2011-10-26

    Type: Initial release

  • Version 1_1: 2012-03-28

    Type: Database references

  • Version 1_2: 2012-10-10

    Type: Database references

  • Version 1_3: 2017-11-08

    Type: Refinement description