1PMY

REFINED CRYSTAL STRUCTURE OF PSEUDOAZURIN FROM METHYLOBACTERIUM EXTORQUENS AM1 AT 1.5 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Refined crystal structure of pseudoazurin from Methylobacterium extorquens AM1 at 1.5 A resolution.

Inoue, T.Kai, Y.Harada, S.Kasai, N.Ohshiro, Y.Suzuki, S.Kohzuma, T.Tobari, J.

(1994) Acta Crystallogr D Biol Crystallogr 50: 317-328

  • DOI: https://doi.org/10.1107/S0907444994000260
  • Primary Citation of Related Structures:  
    1PMY

  • PubMed Abstract: 

    The crystal structure of pseudoazurin from Methylobacterium extorquens AM1 (PAZAM1) has been solved by the molecular replacement method using copper-copper distances as translation parameters, which were obtained from difference Patterson maps calculated with the synchrotron radiation data containing the multiwavelength anomalous-dispersion effect. The structure refinement was carried out by the use of molecular dynamics optimization and the restrained least-squares method. The final crystallographic R factor was 19.9% for the 14 365 reflections greater than 3sigma between 1.5 and 8.0 A resolution. This report describes the characteristic features of the structure of PAZAM 1 as well as the effectiveness of synchrotron radiation for structure analysis of metalloproteins. The environment of the metal active site and the structural differences among blue-copper proteins are discussed.


  • Organizational Affiliation

    Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PSEUDOAZURIN123Methylorubrum extorquensMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P04171 (Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1))
Explore P04171 
Go to UniProtKB:  P04171
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04171
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CU
Query on CU

Download Ideal Coordinates CCD File 
B [auth A]COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Work: 0.199 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.619α = 90
b = 63.28β = 90
c = 35.133γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-07-31
    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: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-08-14
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-02-14
    Changes: Data collection, Database references, Derived calculations