2CCW

Crystal structure of Azurin II at atomic resolution (1.13 angstrom)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.146 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Active Site Structures and the Redox Properties of Blue Copper Proteins: Atomic Resolution Structure of Azurin II and Electronic Structure Calculations of Azurin, Plastocyanin and Stellacyanin.

Paraskevopoulos, K.Sundararajan, M.Surendran, R.Hough, M.A.Eady, R.R.Hillier, I.H.Hasnain, S.S.

(2006) Dalton Trans. 25: 3067

  • DOI: 10.1039/b513942b

  • PubMed Abstract: 
  • Understanding how the active site structures of blue copper proteins determine their redox properties is the central structure-function relationship question of this important class of protein, also referred to as cupredoxins. We here describe both e ...

    Understanding how the active site structures of blue copper proteins determine their redox properties is the central structure-function relationship question of this important class of protein, also referred to as cupredoxins. We here describe both experimental and computational studies of azurin, plastocyanin and stellacyanin designed to define more accurately the geometric structures of the active site of the reduced and oxidized species, and thus to understand how these structures determine the redox potentials of these proteins. To this end the crystal structure of reduced azurin II has been determined at an atomic resolution of 1.13 Angstrom and is presented here. Co-ordinates and structure factors have been deposited in the RCSB Protein Data Bank with accession codes 2ccw and r2ccwsf respectively. The improved accuracy provided by the atomic resolution for the metal stereochemistry are utilised in conjunction with the EXAFS data for theoretical calculations. Multilevel calculations involving density functional theory and molecular mechanical potentials are used to predict both the geometric and electronic structure of the active sites of azurin, plastocyanin and stellacyanin and to estimate the relative redox potentials of these three proteins. We have also compared the relative energies of the structures obtained from experiment at varying resolutions, and from the isolated and embedded cluster calculations. We find significant energy differences between low and high (atomic) resolution structures arising primarily due to inaccuracies in the Cu-ligand distances in the lower resolution structures, emphasising the importance of accurate, very high resolution structural information. QM/MM structures are only approximately 1 kcal mol(-1) lower in energy than the 1.13 Angstrom structure while the optimized gas phase structure is 13.0 kcal mol(-1) lower in energy.


    Organizational Affiliation

    School of Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK L3 5AF.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AZURIN II
A
129Alcaligenes xylosoxydans xylosoxydansMutation(s): 0 
Find proteins for P56275 (Alcaligenes xylosoxydans xylosoxydans)
Go to UniProtKB:  P56275
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CU1
Query on CU1

Download SDF File 
Download CCD File 
A
COPPER (I) ION
Cu
VMQMZMRVKUZKQL-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.13 Å
  • R-Value Free: 0.146 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 51.754α = 90.00
b = 51.754β = 90.00
c = 99.789γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data reduction
HKL-2000data scaling
SHELXL-97refinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-01-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance