3TU6

The Structure of a Pseudoazurin From Sinorhizobium meliltoi

• PDB DOI: https://doi.org/10.2210/pdb3TU6/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Sinorhizobium meliloti
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-09-16 Released: 2012-05-30 
• Deposition Author(s): Laming, E.M., McGrath, A.P., Guss, J.M., Maher, M.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.202 
• R-Value Observed: 0.207 

Literature

The X-ray crystal structure of a pseudoazurin from Sinorhizobium meliloti.

Laming, E.M., McGrath, A.P., Guss, J.M., Kappler, U., Maher, M.J.

(2012) J Inorg Biochem 115: 148-154

• PubMed: 22776735 
• DOI: https://doi.org/10.1016/j.jinorgbio.2012.04.005
• Primary Citation of Related Structures:  
  3TU6


• PubMed Abstract: 
  

  The X-ray crystal structure of oxidised pseudoazurin from the denitrifying plant symbiotic bacterium Sinorhizobium meliloti (SmPAz2) has been solved to a resolution of 2.0 Å. The pseudoazurin from Sinorhizobium sp. is unusual as it forms an operon with a sulfite dehydrogenase enzyme, rather than a Cu nitrite reductase. Examination of the structure reveals that the geometric parameters of the Type I Cu site in SmPAz2 correlate with observed features in the electronic spectrum of the protein. Comparison of the structure of SmPAz2 with those of pseudoazurins from five other bacterial species shows that the surface of SmPAz2 bears a conserved hydrophobic patch encircled by positively-charged residues, which may serve as a recognition site for its redox partners.

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Organizational Affiliation: 

School of Molecular Bioscience, University of Sydney, NSW 2006, Australia.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 13.61 kDa 
• Atom Count: 1,007 
• Modelled Residue Count: 127 
• Deposited Residue Count: 127 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pseudoazurin (Blue copper protein)	A	127	Sinorhizobium meliloti	Mutation(s): 0  Gene Names: azu2, AZU2T, R02830, SMc04047
UniProt
Find proteins for Q92M26 (Rhizobium meliloti (strain 1021)) Explore Q92M26  Go to UniProtKB:  Q92M26

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU	B [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.261 
• R-Value Work: 0.202 
• R-Value Observed: 0.207 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.627	α = 90
b = 53.494	β = 90
c = 59.921	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-05-30 
Deposition Author(s): Laming, E.M., McGrath, A.P., Guss, J.M., Maher, M.J.

Revision History  

• Version 1.0: 2012-05-30
  Type: Initial release
  
• Version 1.1: 2012-07-25
  Changes: Database references
• Version 1.2: 2012-12-19
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations