1PMY | pdb_00001pmy

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

• PDB DOI: https://doi.org/10.2210/pdb1PMY/pdb

• Classification: ELECTRON TRANSFER(CUPROPROTEIN)
• Organism(s): Methylorubrum extorquens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 1994-01-28 Released: 1994-07-31 
• Deposition Author(s): Inoue, T., Kai, Y., Harada, S., Kasai, N., Ohshiro, Y., Suzuki, S., Kohzuma, T., Tobari, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Work: 
  0.199 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

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

• PubMed: 15299445 
• DOI: https://doi.org/10.1107/S0907444994000260
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 13.47 kDa 
• Atom Count: 1,070 
• Modeled Residue Count: 123 
• Deposited Residue Count: 123 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PSEUDOAZURIN	A	123	Methylorubrum extorquens	Mutation(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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	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 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.619	α = 90
b = 63.28	β = 90
c = 35.133	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-07-31 
Deposition Author(s): Inoue, T., Kai, Y., Harada, S., Kasai, N., Ohshiro, Y., Suzuki, S., Kohzuma, T., Tobari, J.

Revision History  

• 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