2WC1 | pdb_00002wc1

Three-dimensional Structure of the Nitrogen Fixation Flavodoxin (NifF) from Rhodobacter capsulatus at 2.2 A

• PDB DOI: https://doi.org/10.2210/pdb2WC1/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rhodobacter capsulatus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2009-03-06 Released: 2010-04-21 
• Deposition Author(s): Perez-Dorado, I., Bittel, C., Hermoso, J.A., Cortez, N., Carrillo, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.267 (Depositor), 0.251 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Structural and Phylogenetic Analysis of Rhodobacter Capsulatus Niff: Uncovering General Features of Nitrogen-Fixation (Nif)-Flavodoxins.

Perez-Dorado, I., Bortolotti, A., Cortez, N., Hermoso, J.A.

(2013) Int J Mol Sci 14: 1152

• PubMed: 23303276 
• DOI: https://doi.org/10.3390/ijms14011152
• Primary Citation Related Structures: 
  2WC1


• PubMed Abstract: 
  

  Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

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Organizational Affiliation: 
• Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Rocasolano", CSIC, Serrano 119, Madrid 28006, Spain. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 20.29 kDa 
• Atom Count: 1,507 
• Modeled Residue Count: 182 
• Deposited Residue Count: 182 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FLAVODOXIN	A	182	Rhodobacter capsulatus	Mutation(s): 0
UniProt
Find proteins for P52967 (Rhodobacter capsulatus (strain ATCC BAA-309 / NBRC 16581 / SB1003)) Explore P52967  Go to UniProtKB:  P52967

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	B [auth A]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.267 (Depositor), 0.251 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.247 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.4	α = 90
b = 66.4	β = 90
c = 121.32	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Perez-Dorado, I., Bittel, C., Hermoso, J.A., Cortez, N., Carrillo, N.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2014-07-30
  Changes: Database references
• Version 1.2: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description