1PVF

E.coli IPP isomerase in complex with diphosphate

Structural Biology Knowledgebase: 1PVF SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.188

Literature

Macromolecules
Sequence Display for 1PVF

Classification: ISOMERASE

Total Structure Weight: 41795.47

Macromolecule Entities
Molecule Chains Length Organism Details
Isopentenyl-diphosphate delta-isomerase A, B 183 Escherichia coli EC#: 5.3.3.2 IUBMB
Gene Name(s): idi ygfV b2889 JW2857
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B DIPHOSPHATE
O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-J
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MN
Query on MN

A, B MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B 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: 1.78 Å
  • R-Value Free: 0.236
  • R-Value Work: 0.188
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.09 α = 90.00
b = 71.88 β = 90.00
c = 91.73 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-06-27
  • Released Date: 2004-07-06
  • Deposition author(s): Wouters, J., Durisotti, V., Oudjama, Y., Stalon, V., Droogmans, L.

Revision History

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