1PVF | pdb_00001pvf

E.coli IPP isomerase in complex with diphosphate

• PDB DOI: https://doi.org/10.2210/pdb1PVF/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 
  0.236 (Depositor) 
• R-Value Work: 
  0.188 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

E.coli Isopentenyl Diphosphate: Dimethylallyl Diphosphate isomerase in complex with diphosphate

Wouters, J., Durisotti, V., Oudjama, Y., Stalon, V., Droogmans, L.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.8 kDa 
• Atom Count: 3,042 
• Modeled Residue Count: 356 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isopentenyl-diphosphate delta-isomerase	A, B	183	Escherichia coli	Mutation(s): 0  Gene Names: IDI OR B2889 EC: 5.3.3.2
UniProt
Find proteins for Q46822 (Escherichia coli (strain K12)) Explore Q46822  Go to UniProtKB:  Q46822

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DPO	E [auth A], H [auth B]	DIPHOSPHATE O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-J
MN	C [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	D [auth A], G [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free:  0.236 (Depositor) 
• R-Value Work:  0.188 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.09	α = 90
b = 71.88	β = 90
c = 91.73	γ = 90

Software Package:

Software Name	Purpose
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2004-07-06
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations