3JS3

Crystal structure of type I 3-dehydroquinate dehydratase (aroD) from Clostridium difficile with covalent reaction intermediate

Structural Biology Knowledgebase: 3JS3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241
  • R-Value Work: 0.189

Literature

Macromolecules
Sequence Display for 3JS3

Classification: LYASE

Total Structure Weight: 117441.64

Macromolecule Entities
Molecule Chains Length Organism Details
3-dehydroquinate dehydratase A, B, C, D 258 Clostridioides difficile EC#: 4.2.1.10 IUBMB
Gene Name(s): aroD CD630_22170
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DHS
Query on DHS

A, B, C, D 3-AMINO-4,5-DIHYDROXY-CYCLOHEX-1-ENECARBOXYLATE
C7 H10 N O4
WPZSUTUAATWRPU-KVQBGUIXSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

Unit Cell:

Length (Å) Angle (°)
a = 60.47 α = 90.00
b = 139.62 β = 90.63
c = 66.77 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-09-09
  • Released Date: 2009-09-22
  • Deposition author(s): Minasov, G., Light, S.H., Shuvalova, L., Dubrovska, I., Winsor, J., Peterson, S.N., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Source and taxonomy | Details: Removed strain from scientific name
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4