2VNP

Monoclinic form of IDI-1

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
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This is version 1.3 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 

    Laboratoire de Chimie Biologique Structurale, FUNDP University of Namur, 61 Rue de Bruxelles, 5000 Namur, Belgium. [email protected]


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ISOPENTENYL-DIPHOSPHATE DELTA-ISOMERASE
A, B
183Escherichia coli BL21Mutation(s): 0 
EC: 5.3.3.2
UniProt
Find proteins for Q46822 (Escherichia coli (strain K12))
Explore Q46822 
Go to UniProtKB:  Q46822
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ46822
Sequence Annotations
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  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding 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 = 43.2α = 90
b = 69.1β = 100.3
c = 62.4γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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