Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.70 kDa 
• Atom Count: 2757 
• Residue Count: 336 
• Unique protein chains: 1

1HAU

X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION

• DOI: 10.2210/pdb1HAU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Achromobacter xylosoxidans
• Mutation(s): No 


• Deposited: 2001-04-09 Released: 2001-08-02 
• Deposition Author(s): Ellis, M.J., Dodd, F.E., Strange, R.W., Prudencio, M., Sawerseady, R.R., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 

Literature

X-Ray Structure of a Blue Copper Nitrite Reductase at High Ph and in Copper-Free Form at 1.9 A Resolution

Ellis, M.J., Dodd, F.E., Strange, R.W., Prudencio, M., Sawers, G., Eady, R.R., Hasnain, S.S.

(2001) Acta Crystallogr D Biol Crystallogr 57: 1110

• PubMed: 11468394 
• DOI: 10.1107/s0907444901008654
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Copper-containing nitrite reductases possess a trimeric structure where the catalytic Cu site, located at the monomer-monomer interface, resembles the catalytic sites of a number of Zn enzymes. Nitrite reductase from Alcaligenes xylosoxidans has optimum activity at pH 5.2 which decreases to a negligible level at pH 8. The structure of this nitrite reductase has previously been determined at pH 4.6. It has now been crystallized under new conditions at pH 8.5. Its crystallographic structure provides a structural explanation for the greatly reduced activity of the enzyme at high pH. Characterization of overexpressed protein in solution by EXAFS suggested that the protein lacked Cu in the catalytic type 2 Cu site and that the site was most probably occupied by Zn. Using the anomalous signals from Cu and Zn, the crystal structure revealed that the expressed protein was devoid of Cu in the catalytic site and that only a trace amount (<10%) of Zn was present at this site in the crystal. Despite the close structural similarity of the catalytic site to a number of Zn enzymes, these data suggest that Zn, if it binds at the catalytic copper site, binds weakly in nitrite reductase.

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Organizational Affiliation: 

Synchrotron Radiation Department, CLRC Daresbury Laboratory, Warrington WA4 4AD, England.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE	A	336	Achromobacter xylosoxidans	Mutation(s): 0  Gene Names: nir, nirK, ERS451415_02178 EC: 1.7.99.3 (PDB Primary Data), 1.7.2.1 (PDB Primary Data)
Find proteins for O68601 (Alcaligenes xylosoxydans xylosoxydans) Go to UniProtKB:  O68601

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU	A	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.190 
• R-Value Work: 0.154 
• R-Value Observed: 0.156 
• Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.978	α = 90
b = 80.978	β = 90
c = 99.781	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2001-04-09 
• Released Date: 2001-08-02 
Deposition Author(s): Ellis, M.J., Dodd, F.E., Strange, R.W., Prudencio, M., Sawerseady, R.R., Hasnain, S.S.

Revision History 

• Version 1.0: 2001-08-02
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance