2VNP

Monoclinic form of IDI-1

• PDB DOI: https://doi.org/10.2210/pdb2VNP/pdb
• Entry: 2VNP supersedes: 2VEH

• Classification: ISOMERASE
• Organism(s): Escherichia coli BL21
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2008-02-06 Released: 2008-03-18 
• Deposition Author(s): de Ruyck, J., Oudjama, Y., Wouters, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.255 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Monoclinic Form of Isopentenyl Diphosphate Isomerase: A Case of Polymorphism in Biomolecular Crystals.

De Ruyck, J., Oudjama, Y., Wouters, J.

(2008) Acta Crystallogr Sect F Struct Biol Cryst Commun 64: 239

• PubMed: 18391416 
• DOI: https://doi.org/10.1107/S174430910800568X
• Primary Citation of Related Structures:  
  2VNP, 2VNQ


• PubMed Abstract: 
  

  Type 1 isopentenyl diphosphate isomerase (IDI-1) has been crystallized in a new crystal form. After data collection from small thin needle-shaped crystals, a new monoclinic form of the studied protein was identified. In this article, the three crystal forms of IDI-1 (orthorhombic, monoclinic and trigonal) are compared.

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Organizational Affiliation: 

Laboratoire de Chimie Biologique Structurale, FUNDP University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 41.95 kDa 
• Atom Count: 2,914 
• Modelled 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 BL21	Mutation(s): 0  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
DED	E [auth A], H [auth B]	2-DIMETHYLAMINO-ETHYL-DIPHOSPHATE C4 H13 N O7 P2 QGKJQRINUQGSJM-UHFFFAOYSA-N
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

Binding Affinity Annotations
ID	Source	Binding Affinity
DED	PDBBind:  2VNP	Ki: 0.12 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.255 
• R-Value Work: 0.194 
• R-Value Observed: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.2	α = 90
b = 69.1	β = 100.3
c = 62.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-03-18 
Deposition Author(s): de Ruyck, J., Oudjama, Y., Wouters, J.
• This entry supersedes: 2VEH

Revision History  

• Version 1.0: 2008-03-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description