1AZC

STRUCTURE OF APO-AZURIN FROM ALCALIGENES DENITRIFICANS AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of apo-azurin from Alcaligenes denitrificans at 1.8 A resolution.

Shepard, W.E.Kingston, R.L.Anderson, B.F.Baker, E.N.

(1993) Acta Crystallogr.,Sect.D 49: 331-343

  • DOI: 10.1107/S0907444992013544
  • Primary Citation of Related Structures:  1AIZ, 1AZB

  • PubMed Abstract: 
  • The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on cryst ...

    The structure of apo-azurin from Alcaligenes denitrificans has been determined at high resolution by X-ray crystallography. Two separate structure analyses have been carried out, (i) on crystals obtained from solutions of apo-azurin and (ii) on crystals obtained by removal of copper from previously formed crystals of holo-azurin. Data to 1.8 A resolution were collected from the apo-azurin crystals, by Weissenberg photography (with image plates) using synchrotron radiation and by diffractometry, and the structure was refined by restrained least-squares methods to a final R value of 0.160 for all data in the range 10.0-1.8 A. The final model of 1954 protein atoms, 246 water molecules (66 half-weighted), four SO(4)(2-) ions, and two low-occupancy (0.13 and 0.15) Cu atoms has r.m.s. deviations of 0.012, 0.045 and 0.013 A from standard bond lengths, angle distances and planar groups. For copper-removed azurin, data to 2.2 A were collected by diffractometry and the structure refined by restrained least squares to a final R value of 0.158 for all data in the range 10.0-2.2 A. The final model of 1954 protein atoms, 264 water molecules, two SO(4)(2-) ions, two low occupancy (0.18 and 0.22) metal atoms and one unidentified atom (modelled as S) has r.m.s. deviations of 0.013, 0.047 and 0.012 A from standard bond lengths, angle distances and planar groups. The two structures are essentially identical to each other and show no significant differences from the oxidized and reduced holo-azurin structures. The ligand side chains move slightly closer together following the removal of copper, with the radius of the cavity between the three strongly binding ligands, His 46, His 117 and Cys 112, shrinking from 1.31 A in reduced azurin to 1.24 A in oxidized azurin and 1.16 A in apo-azurin. There is a suggestion of increased flexibility in one of the copper-binding loops but the structure supports the view that the copper site found in holo-azurin is a stable structure, defined by the constraints of the polypeptide structure even in the absence of a bound metal ion.


    Related Citations: 
    • Structure of Azurin from Alcaligenes Denitrificans at 2.5 Angstroms Resolution
      Norris, G.E.,Anderson, B.F.,Baker, E.N.
      (1983) J.Mol.Biol. 165: 501
    • Structure of Azurin from Alcaligenes Denitrificans Refinement at 1.8 Angstroms Resolution and Comparison of the Two Crystallographically Independent Molecules
      Baker, E.N.
      (1988) J.Mol.Biol. 203: 1071
    • Copper Coordination Geometry in Azurin Undergoes Minimal Change on Reduction of Copper(II) to Copper (I)
      Shepard, W.E.B.,Anderson, B.F.,Lewandoski, D.A.,Norris, G.E.,Baker, E.N.
      (1990) J.Am.Chem.Soc. 112: 7817
    • Purification and Preliminary Crystallographic Studies on Azurin and Cytochrome C' from Alcaligenes Denitrificans and Alcaligenes Sp. Ncib 11015
      Norris, G.E.,Anderson, B.F.,Baker, E.N.,Rumball, S.V.
      (1979) J.Mol.Biol. 135: 309


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Massey University, Palmerston North, New Zealand.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AZURIN
A, B
129Achromobacter denitrificansGene Names: azu
Find proteins for P00280 (Achromobacter denitrificans)
Go to UniProtKB:  P00280
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 75.100α = 90.00
b = 74.100β = 90.00
c = 99.500γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other