1JDF

Glucarate Dehydratase from E.coli N341D mutant

Structural Biology Knowledgebase: 1JDF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1JDF

Classification: LYASE

Total Structure Weight: 198131.70

Macromolecule Entities
Molecule Chains Length Organism Details
Glucarate Dehydratase A, B, C, D 446 Escherichia coli EC#: 4.2.1.40 IUBMB
Mutation: N341D
Gene Name(s): gudD ygcX b2787 JW2758
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C, D 2,3-DIHYDROXY-5-OXO-HEXANEDIOATE
C6 H6 O7
QUURPCHWPQNNGL-ZAFYKAAXSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IPA
Query on IPA

A, B, C, D ISOPROPYL ALCOHOL
2-PROPANOL (Synonym)
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.198
  • Space Group: P 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.93 α = 104.11
b = 83.93 β = 93.75
c = 98.22 γ = 113.12

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-06-13
  • Released Date: 2001-09-05
  • Deposition author(s): Gulick, A.M., Hubbard, B.K., Gerlt, J.A., Rayment, I.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4