1RDG

RUBREDOXIN FROM DESULFOVIBRIO GIGAS. A MOLECULAR MODEL OF THE OXIDIZED FORM AT 1.4 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Observed: 0.136 

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This is version 1.2 of the entry. See complete history


Literature

Rubredoxin from Desulfovibrio gigas. A molecular model of the oxidized form at 1.4 A resolution.

Frey, M.Sieker, L.Payan, F.Haser, R.Bruschi, M.Pepe, G.LeGall, J.

(1987) J Mol Biol 197: 525-541

  • DOI: 10.1016/0022-2836(87)90562-6
  • Primary Citation of Related Structures:  
    1RDG

  • PubMed Abstract: 
  • The crystal structure of rubredoxin from the sulfate-reducing bacterium Desulfovibrio gigas has been determined at 1.4 A resolution (1 A = 0.1 nm) by X-ray diffraction methods; starting with a model of the isostructural rubredoxin from Desulfovibrio ...

    The crystal structure of rubredoxin from the sulfate-reducing bacterium Desulfovibrio gigas has been determined at 1.4 A resolution (1 A = 0.1 nm) by X-ray diffraction methods; starting with a model of the isostructural rubredoxin from Desulfovibrio vulgaris. Refinement of the molecular model has been carried out by restrained least-squares techniques and Fourier series calculations. The present model includes a formyl at the N-terminal end and 121 possible sites for solvent molecules with full or partial occupancy, which corresponds to the modeling of nearly all the solvent medium. The crystallographic R factor against the data with 10 A greater than d greater than 1.4 A with F greater than 2 sig(F), is 0.136; and R = 0.140 when all the data are considered. The estimated average root-mean-square (r.m.s.) error on the positional parameters is about 0.12 A. The overall structural features of this molecule are close to those of the two highly refined rubredoxins from Clostridium pasteurianum and D. vulgaris. Superposition of these two molecules on the rubredoxin from D. gigas shows in both cases an overall r.m.s. deviation of 0.5 A for the atoms in the main-chain and of 0.4 A for the atoms in the side-chains that make up the hydrophobic core. The iron atom is co-ordinated to four cysteine sulfur atoms forming an almost regular tetrahedron, with Fe-SG distances ranging from 2.27 A to 2.31 A and angles varying from 103 degrees to 115 degrees. The intramolecular hydrogen-bonding pattern is quite comparable to those found in other proteins refined at high resolution. All the polar groups are involved in hydrogen bonds: intramolecular, intermolecular or with solvent molecules. The main structural differences from the other rubredoxins are in the nature and the distribution of some of the charged residues over the molecular surface. The possible influence of several structural factors on the intramolecular and intermolecular electron transfer properties such as the NH...SG bonds, the solvent exposure of the redox center, and the aromatic core is discussed. The conservation, during evolution, of a ring of acidic residues in the proximity of the FeSG4 center suggests that this ring may be implicated in the recognition processes between rubredoxins and their functional partners.


    Related Citations: 
    • Some Comparisons between Two Crystallized Anaerobic Bacterial Rubredoxins from Desulfovibrio Gigas and D. Vulgaris
      Pierrot, M., Haser, R., Frey, M., Bruschi, M., Legall, J., Sieker, L.C., Jensen, L.H.
      (1976) J Mol Biol 107: 179
    • The Amino Acid Sequence of Rubredoxin from the Sulfate Reducing Bacterium, Desulfovibrio Gigas
      Bruschi, M.
      (1976) Biochem Biophys Res Commun 70: 615

    Organizational Affiliation

    CRMC2-CNRS Campus, Marseille, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RUBREDOXINA52Desulfovibrio gigasMutation(s): 0 
Find proteins for P00270 (Desulfovibrio gigas)
Explore P00270 
Go to UniProtKB:  P00270
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download CCD File 
A
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
FOR
Query on FOR

Download CCD File 
A
FORMYL GROUP
C H2 O
WSFSSNUMVMOOMR-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Observed: 0.136 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 19.731α = 90
b = 41.67β = 109.4
c = 24.394γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1989-04-19
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance