1WAE | pdb_00001wae

Crystal structure of H129V Mutant of Alcaligenes Xylosoxidans Nitrite Reductase

• PDB DOI: https://doi.org/10.2210/pdb1WAE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Achromobacter xylosoxidans
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-10-26 Released: 2004-10-28 
• Deposition Author(s): Ellis, M.J., Antonyuk, S.V., Strange, R.W., Sawers, G., Eady, R.R., Hasnain, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.201 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Observation of an Unprecedented Cu Bis-His Site: Crystal Structure of the H129V Mutant of Nitrite Reductase

Ellis, M.J., Antonyuk, S.V., Strange, R.W., Sawers, G., Eady, R.R., Hasnain, S.S.

(2004) Inorg Chem 43: 7591

• PubMed: 15554622 
• DOI: https://doi.org/10.1021/ic048966p
• Primary Citation Related Structures: 
  1WAE


• PubMed Abstract: 
  

  Copper nitrite reductases contain both an electron-transfer type 1 Cu site and a catalytic type 2 Cu site. We have mutated one of the type 2 copper ligating histidines to observe the effect on catalytic turnover. This mutation has created a unique site where Cu is ligated by 2 His Nepsilon2 atoms alone.

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Organizational Affiliation: 
• Molecular Biophysics Group, CCLRC Daresbury Laboratory, Warrington, Cheshire, UK.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 36.72 kDa 
• Atom Count: 2,727 
• Modeled Residue Count: 334 
• Deposited Residue Count: 336 
• Unique protein chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CU	B [auth A], C [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.226 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.201 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.206	α = 90
b = 91.206	β = 90
c = 145.866	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-28 
Deposition Author(s): Ellis, M.J., Antonyuk, S.V., Strange, R.W., Sawers, G., Eady, R.R., Hasnain, S.S.

Revision History  

• Version 1.0: 2004-10-28
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Database references, Derived calculations, Non-polymer description, Other, Structure summary, Version format compliance
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description