3VAB

Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP

Structural Biology Knowledgebase: 3VAB SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.221

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3VAB

Classification: lyase

Total Structure Weight: 96731.06

Macromolecule Entities
Molecule Chains Length Organism Details
Diaminopimelate decarboxylase 1 A, B 443 Brucella melitensis EC#: 4.1.1.20 IUBMB
Gene Name(s): lysA BMEI0084

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
SO4
Query on SO4

A SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
EDO
Query on EDO

A, B 1,2-ETHANEDIOL
ETHYLENE GLYCOL (Synonym)
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
LLP
Query on LLP
A, B L-PEPTIDE LINKING C14 H22 N3 O7 P LYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.268
  • R-Value Work: 0.221
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 59.53 α = 90.00
b = 126.37 β = 112.71
c = 68.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-12-29
  • Released Date: 2012-01-18
  • Deposition author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History

No revisions since initial release