Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.88 kDa 
• Atom Count: 2560 
• Modelled Residue Count: 290 
• Deposited Residue Count: 292 
• Unique protein chains: 1

4HEQ

The crystal structure of flavodoxin from Desulfovibrio gigas

• PDB DOI: 10.2210/pdb4HEQ/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Desulfovibrio gigas
• Mutation(s): No 


• Deposited: 2012-10-04 Released: 2013-01-30 
• Deposition Author(s): Hsieh, Y.C., Chen, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.211 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Literature

Crystal Structure of Dimeric Flavodoxin from Desulfovibrio gigas Suggests a Potential Binding Region for the Electron-Transferring Partner

Hsieh, Y.C., Chia, T.S., Fun, H.K., Chen, C.J.

(2013) Int J Mol Sci 14: 1667-1683

• PubMed: 23322018 
• DOI: 10.3390/ijms14011667
• Primary Citation of Related Structures:  
  4HEQ


• PubMed Abstract: 
  

Flavodoxins, which exist widely in microorganisms, have been found in various pathways with multiple physiological functions. The flavodoxin (Fld) containing the cofactor flavin mononucleotide (FMN) from sulfur-reducing bacteria Desulfovibrio gigas (D. gigas) is a short-chain enzyme that comprises 146 residues with a molecular mass of 15 kDa and plays important roles in the electron-transfer chain. To investigate its structure, we purified this Fld directly from anaerobically grown D. gigas cells. The crystal structure of Fld, determined at resolution 1.3 Å, is a dimer with two FMN packing in an orientation head to head at a distance of 17 Å, which generates a long and connected negatively charged region. Two loops, Thr59-Asp63 and Asp95-Tyr100, are located in the negatively charged region and between two FMN, and are structurally dynamic. An analysis of each monomer shows that the structure of Fld is in a semiquinone state; the positions of FMN and the surrounding residues in the active site deviate. The crystal structure of Fld from D. gigas agrees with a dimeric form in the solution state. The dimerization area, dynamic characteristics and structure variations between monomers enable us to identify a possible binding area for its functional partners.

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Organizational Affiliation: 

Life Science Group, Scientific Research Division, National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Flavodoxin	A, B	146	Desulfovibrio gigas	Mutation(s): 0
UniProt
Find proteins for Q01095 (Megalodesulfovibrio gigas (strain ATCC 19364 / DSM 1382 / NCIMB 9332 / VKM B-1759)) Explore Q01095  Go to UniProtKB:  Q01095

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.211 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.198	α = 90
b = 60.366	β = 90
c = 76.246	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-04 
• Released Date: 2013-01-30 
Deposition Author(s): Hsieh, Y.C., Chen, C.J.

Revision History  

• Version 1.0: 2013-01-30
  Type: Initial release