1XXX

Crystal structure of Dihydrodipicolinate Synthase (DapA, Rv2753c) from Mycobacterium tuberculosis

Structural Biology Knowledgebase: 1XXX SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.148

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XXX

Classification: LYASE

Total Structure Weight: 250637.47

Macromolecule Entities
Molecule Chains Length Organism Details
Dihydrodipicolinate synthase A, B, C..., D, E, F, G, HA, B, C, D, E, F, G, H 303 Mycobacterium tuberculosis EC#: 4.3.3.7 IUBMB
Mutation: M1V
Gene Name(s): dapA Rv2753c MTV002.18c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D, E, F, G, H 2,3-DIHYDROXY-1,4-DITHIOBUTANE
1,4-DITHIOTHREITOL (Synonym)
C4 H10 O2 S2
VHJLVAABSRFDPM-IMJSIDKUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B, C, D, E, F, G, H CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B, C, D, E, F, G, H MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 0.215
  • R-Value Work: 0.148
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 94.79 α = 90.00
b = 87.37 β = 107.78
c = 139.85 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-11-09
  • Released Date: 2006-02-14
  • Deposition author(s): Kefala, G., Panjikar, S., Janowski, R., Weiss, M.S., TB Structural Genomics Consortium (TBSGC)

Revision History

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