1BQK | pdb_00001bqk

OXIDIZED PSEUDOAZURIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.190 (Depositor) 
  • R-Value Work: 
    0.178 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history

Literature

Crystal structure determinations of oxidized and reduced pseudoazurins from Achromobacter cycloclastes. Concerted movement of copper site in redox forms with the rearrangement of hydrogen bond at a remote histidine.

Inoue, T.Nishio, N.Suzuki, S.Kataoka, K.Kohzuma, T.Kai, Y.

(1999) J Biological Chem 274: 17845-17852

  • DOI: https://doi.org/10.1074/jbc.274.25.17845
  • Primary Citation Related Structures: 
    1BQK, 1BQR

  • PubMed Abstract: 

    The crystal structures of oxidized and reduced pseudoazurins from a denitrifying bacterium, Achromobacter cycloclastes IAM1013, have been determined at 1.35- and 1.6-A resolutions, respectively. The copper site in the oxidized state exhibits a distorted tetrahedral structure like those of other pseudoazurins. However, not only a small change of the copper geometry, but concerted peptide bond flips are identified. The imidazole ring of remote His6 has a hydrogen bonding distance of 2.73 A between N-delta1(His6) and O-gamma1(Thr36) in the oxidized protein. When the protein is reduced at pH 6.0, the imidazole ring rotates by 30.3 degrees and moves 1.00 A away from the position of the oxidized state. A new hydrogen bond between N-epsilon2(His6) and O-epsilon1(Glu4) is formed with a distance of 3.03 A, while the hydrogen bond between N-delta1(His6)-O-gamma1(Thr36) is maintained with an interatomic distance of 2.81 A. A concomitant peptide bond flip of main chain between Ile34 and Thr36 occurs.


  • Organizational Affiliation
    • Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.

Macromolecule Content 

  • Total Structure Weight: 13.1 kDa 
  • Atom Count: 1,035 
  • Modeled Residue Count: 124 
  • Deposited Residue Count: 124 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PSEUDOAZURIN124Achromobacter cycloclastesMutation(s): 0 
UniProt
Find proteins for P19567 (Achromobacter cycloclastes)
Explore P19567 
Go to UniProtKB:  P19567
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19567
Sequence Annotations
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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: 1.35 Å
  • R-Value Free:  0.190 (Depositor) 
  • R-Value Work:  0.178 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.731α = 90
b = 61.544β = 90
c = 30.083γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-08-17
    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: 2023-08-09
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-05-22
    Changes: Data collection