1IDQ | pdb_00001idq

CRYSTAL STRUCTURE OF NATIVE VANADIUM-CONTAINING CHLOROPEROXIDASE FROM CURVULARIA INAEQUALIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Work: 
    0.170 (Depositor), 0.159 (DCC) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Implications for the catalytic mechanism of the vanadium-containing enzyme chloroperoxidase from the fungus Curvularia inaequalis by X-ray structures of the native and peroxide form.

Messerschmidt, A.Prade, L.Wever, R.

(1997) Biol Chem 378: 309-315

  • DOI: https://doi.org/10.1515/bchm.1997.378.3-4.309
  • Primary Citation Related Structures: 
    1IDQ, 1IDU

  • PubMed Abstract: 

    Implications for the catalytic mechanism of the vanadium-containing chloroperoxidase from the fungus Curvularia inaequalis have been obtained from the crystal structures of the native and peroxide forms of the enzyme. The X-ray structures have been solved by difference Fourier techniques using the atomic model of the azide chloroperoxidase complex. The 2.03 A crystal structure (R = 19.7%) of the native enzyme reveals the geometry of the intact catalytic vanadium center. The vanadium is coordinated by four non-protein oxygen atoms and one nitrogen (NE2) atom from histidine 496 in a trigonal bipyramidal fashion. Three oxygens are in the equatorial plane and the fourth oxygen and the nitrogen are at the apexes of the bipyramid. In the 2.24 A crystal structure (R = 17.7%) of the peroxide derivate the peroxide is bound to the vanadium in an eta2-fashion after the release of the apical oxygen ligand. The vanadium is coordinated also by 4 non-protein oxygen atoms and one nitrogen (NE2) from histidine 496. The coordination geometry around the vanadium is that of a distorted tetragonal pyramid with the two peroxide oxygens, one oxygen and the nitrogen in the basal plane and one oxygen in the apical position. A mechanism for the catalytic cycle has been proposed based on these X-ray structures and kinetic data.


  • Organizational Affiliation
    • Max-Planck-Institut für Biochemie, Martinsried bei München, Germany.

Macromolecule Content 

  • Total Structure Weight: 67.74 kDa 
  • Atom Count: 4,938 
  • Modeled Residue Count: 574 
  • Deposited Residue Count: 609 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VANADIUM CHLOROPEROXIDASE609Curvularia inaequalisMutation(s): 0 
EC: 1.11.1.10
UniProt
Find proteins for P49053 (Curvularia inaequalis)
Explore P49053 
Go to UniProtKB:  P49053
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49053
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VO4

Query on VO4



Download:Ideal Coordinates CCD File
B [auth A]VANADATE ION
O4 V
LSGOVYNHVSXFFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.03 Å
  • R-Value Work:  0.170 (Depositor), 0.159 (DCC) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.72α = 90
b = 131.72β = 90
c = 112.46γ = 120
Software Package:
Software NamePurpose
CCP4:model building
FFTmodel building
X-PLORrefinement
MOSFLMdata reduction
CCP4data scaling
ROTAVATAdata scaling
CCP4phasing
SFCALCphasing
FFTphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-04-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Advisory, Refinement description
  • Version 1.4: 2023-08-09
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description