1DYZ | pdb_00001dyz

OXIDISED AZURIN II FROM ALCALIGENES XYLOSOXIDANS

• PDB DOI: https://doi.org/10.2210/pdb1DYZ/pdb
• Entry: 1DYZ supersedes: 1ARN

• Classification: ELECTRON TRANSPORT
• Organism(s): Achromobacter xylosoxidans
• Mutation(s): No 


• Deposited: 2000-02-11 Released: 2000-07-10 
• Deposition Author(s): Dodd, F.E., Abraham, Z.H.L., Eady, R.R., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.205 (Depositor) 
• R-Value Work: 
  0.189 (Depositor), 0.204 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

Structures of Oxidised and Reduced Azurin II from Alcaligenes Xylosoxidans at 1.75 Angstoms Resolution

Dodd, F.E., Abraham, Z.H.L., Eady, R.R., Hasnain, S.S.

(2000) Acta Crystallogr D Biol Crystallogr 56: 690

• PubMed: 10818345 
• DOI: https://doi.org/10.1107/s0907444900003309
• Primary Citation Related Structures: 
  1DYZ, 1DZ0


• PubMed Abstract: 
  

  Crystallographic structures of oxidized and reduced forms of azurin II are reported at 1.75 A resolution. Data were collected using one crystal in each case and by translating the crystal after each oscillation range to minimize photoreduction. Very small differences are observed at the Cu site upon reduction and these cannot be determined with confidence at current resolution. A comparison with the three-dimensional EXAFS reveals a good correspondence for all the ligand distances except for Cu-His46, where a larger deviation of approximately 0.12-0.18 A is observed, indicating that this ligand is more tightly restrained in the crystallographic refinement at the current resolution.

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Organizational Affiliation: 
• Synchrotron Radiation Department, CCLRC Daresbury Laboratory, Warrington, England.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 13.86 kDa 
• Atom Count: 1,024 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AZURIN II	A	129	Achromobacter xylosoxidans	Mutation(s): 0
UniProt
Find proteins for P56275 (Alcaligenes xylosoxydans xylosoxydans) Explore P56275  Go to UniProtKB:  P56275

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: 1.75 Å
• R-Value Free:  0.205 (Depositor) 
• R-Value Work:  0.189 (Depositor), 0.204 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.65	α = 90
b = 52.65	β = 90
c = 100.63	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
WEIS	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-07-10 
Deposition Author(s): Dodd, F.E., Abraham, Z.H.L., Eady, R.R., Hasnain, S.S.
• This entry supersedes: 1ARN

Revision History  

• Version 1.0: 2000-07-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2023-12-06
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.3: 2024-11-20
  Changes: Structure summary