3NJ2

Crystal structure of cce_0566 from the cyanobacterium Cyanothece 51142, a protein associated with nitrogen fixation from the DUF269 family

• PDB DOI: https://doi.org/10.2210/pdb3NJ2/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Crocosphaera subtropica ATCC 51142
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-06-16 Released: 2010-07-07 
• Deposition Author(s): Robinson, H., Ralston, C.Y., Addlagatta, A., Buchko, G.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.255 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 

Literature

Crystal structure of cce_0566 from Cyanothece 51142, a protein associated with nitrogen fixation in the DUF269 family.

Buchko, G.W., Robinson, H.

(2012) FEBS Lett 586: 350-355

• PubMed: 22289180 
• DOI: https://doi.org/10.1016/j.febslet.2012.01.037
• Primary Citation of Related Structures:  
  3NJ2


• PubMed Abstract: 
  

  The crystal structure for cce_0566 (171 aa, 19.4 kDa), a DUF269 annotated protein from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142, was determined to 1.60Å resolution. Cce_0566 is a homodimer with each molecule composed of eight α-helices folded on one side of a three strand anti-parallel β-sheet. Hydrophobic interactions between the side chains of largely conserved residues on the surface of each β-sheet hold the dimer together. The fold observed for cce_0566 may be unique to proteins in the DUF269 family, hence, the protein may also have a function unique to nitrogen fixation. A solvent accessible cleft containing conserved charged residues near the dimer interface could represent the active site or ligand-binding surface for the protein's biological function.

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Organizational Affiliation: 

Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 39.46 kDa 
• Atom Count: 2,736 
• Modelled Residue Count: 303 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF269-containing protein	A, B	174	Crocosphaera subtropica ATCC 51142	Mutation(s): 0  Gene Names: cce_0566
UniProt
Find proteins for B1WPD5 (Crocosphaera subtropica (strain ATCC 51142 / BH68)) Explore B1WPD5  Go to UniProtKB:  B1WPD5

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.59 Å
• R-Value Free: 0.255 
• R-Value Work: 0.210 
• R-Value Observed: 0.212 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.079	α = 90
b = 44.573	β = 111.01
c = 67.724	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-07 
Deposition Author(s): Robinson, H., Ralston, C.Y., Addlagatta, A., Buchko, G.W.

Revision History  

• Version 1.0: 2010-07-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.2: 2012-02-22
  Changes: Database references
• Version 1.3: 2012-02-29
  Changes: Database references
• Version 1.4: 2023-09-06
  Changes: Data collection, Database references, Refinement description