1A2V | pdb_00001a2v

COPPER AMINE OXIDASE FROM HANSENULA POLYMORPHA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 
    0.224 (Depositor) 
  • R-Value Work: 
    0.184 (Depositor) 
  • R-Value Observed: 
    0.184 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Crystallographic study of yeast copper amine oxidase.

Li, R.Chen, L.Cai, D.Klinman, J.P.Mathews, F.S.

(1997) Acta Crystallogr D Biol Crystallogr 53: 364-370

  • DOI: https://doi.org/10.1107/S0907444997000814
  • Primary Citation Related Structures: 
    1A2V

  • PubMed Abstract: 

    The copper-containing amine oxidase from the yeast Hansenula polymorpha (YAO) has been crystallized and partially solved by molecular replacement. It catalyzes the oxidative deamination of primary amines by molecular oxygen to the corresponding aldehydes, ammonia and hydrogen peroxide. It contains a covalently bound redox cofactor, topa quinone, generated by post-translational modification of a single tyrosine side chain. The crystals of YAO are orthorhombic, with space-group symmetry P2(1)2(1)2(1) and unit-cell dimensions a = 138.8, b = 148.2, c = 234.0 A and diffract X-rays beyond 2.0 A resolution. Solution by molecular replacement using the E. coli amine oxidase structure [Parsons, Convery, Wilmot, Yadav, Blakeley, Corner, Philips, McPherson & Knowles (1995). Structure, 3, 1171-1184] as a search model reveals that there are three dimers in the asymmetric unit in a trigonal arrangement having 32 point-group symmetry. The solution agrees well with the self-rotation function of YAO. The non-crystallographic threefold axis lies parallel to a crystallographic twofold screw axis and each dimer has twofold symmetry. Phases from the refined model based on the molecular-replacement solution were used to solve one heavy-atom derivative. Model building from the unbiased isomorphous replacement phases is in progress.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA.

Macromolecule Content 

  • Total Structure Weight: 442.52 kDa 
  • Atom Count: 33,726 
  • Modeled Residue Count: 3,930 
  • Deposited Residue Count: 3,930 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
METHYLAMINE OXIDASE
A, B, C, D, E
A, B, C, D, E, F
655Ogataea angustaMutation(s): 1 
EC: 1.4.3.6 (PDB Primary Data), 1.4.3.21 (UniProt)
UniProt
Find proteins for P12807 (Pichia angusta)
Explore P12807 
Go to UniProtKB:  P12807
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12807
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free:  0.224 (Depositor) 
  • R-Value Work:  0.184 (Depositor) 
  • R-Value Observed: 0.184 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 138.77α = 90
b = 148.22β = 90
c = 234.01γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEITdata reduction
X-PLORmodel building
X-PLORrefinement
SCALEITdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-02
    Changes: Database references, Derived calculations, Refinement description