3FX2

COMPARISON OF THE CRYSTAL STRUCTURES OF A FLAVODOXIN IN ITS THREE OXIDATION STATES AT CRYOGENIC TEMPERATURES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Comparison of the crystal structures of a flavodoxin in its three oxidation states at cryogenic temperatures.

Watt, W.Tulinsky, A.Swenson, R.P.Watenpaugh, K.D.

(1991) J.Mol.Biol. 218: 195-208

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The focus of this study has been to determine the conformation of the holoprotein of recombinant flavodoxin from Desulfovibrio vulgaris with the FMN in each of its three oxidation states. The structures of the oxidized state of the wild-type flavodox ...

    The focus of this study has been to determine the conformation of the holoprotein of recombinant flavodoxin from Desulfovibrio vulgaris with the FMN in each of its three oxidation states. The structures of the oxidized state of the wild-type flavodoxin at 2.0 A from D. vulgaris was used as a starting model for refinement. Diffraction experiments were conducted at low temperature (-150 degrees C) in order to maintain the oxidation state of interest throughout the intensity data collection. yellow bipyramids by the standard hanging-drop method from 3.2 M-ammonium sulfate in 0.1 M-Tris-HCl buffer at pH 7.0 with protein concentrations ranging from 0.7% to 0.9%. The reduced states of the crystals were achieved through the addition of sodium dithionite at pH 7.0 for the semiquinone (semi-reduced) and at pH 9.0 for the hydroquinone (fully reduced). Data sets consisting of one at room temperature (oxidized state) and three at low temperature (each oxidation state) were collected on a Nicolet P3F/Xentronics area detector X-ray diffractometer system. The four structures, hydroquinone at 2.25 A resolution and all others at 1.9 A resolution, were refined by the restrained parameter least-squares program PROLSQ. The final crystallographic R-values converged to 0.21 (hydroquinone), 0.20 (semiquinone), 0.20 (oxidized, low temperature), and 0.17 (oxidized, room temperature). The reduced states of flavodoxin show a different conformation of the protein polypeptide chain (Asp61-Gly62) in the vicinity of NH(5) of the isoalloxazine group relative to the oxidized state. However, there are only slight conformational differences between the semiquinone and hydroquinone states. In this report, structural comparisons of the three are made, with particular emphasis on the features that might be related to the difference in temperature of the diffraction data collections and differences in the oxidation state of the FMN.


    Related Citations: 
    • Structure of the Oxidized Form of a Flavodoxin at 2.5-Angstroms Resolution. Resolution of the Phase Ambiguity by Anomalous Scattering
      Watenpaugh, K.D.,Sieker, L.C.,Jensen, L.H.,Legall, J.,Dubourdieu, M.
      (1972) Proc.Natl.Acad.Sci.USA 69: 3185
    • Cloning, Nucleotide Sequence, and Expression of the Flavodoxin Gene from Disulfovibrio Vulgaris (Hildenborough)
      Krey, G.D.,Vanin, E.F.,Swenson, R.P.
      (1988) J.Biol.Chem. 218: 15436
    • A Crystallographic Structural Study of the Oxidation States of Desulfovibrio Vulgaris Flavodoxin
      Watenpaugh, K.D.,Sieker, L.C.,Jensen, L.H.
      (1976) Flavins and Flavoproteins --: 405
    • Flavin Mononucleotide Conformation and Environment in Flavodoxin from Desulfovibrio Vulgaris
      Watenpaugh, K.D.,Sieker, L.C.,Jensen, L.H.
      (1975) STRUCTURE AND CONFORMATION OF NUCLEIC ACIDS AND PROTEIN-NUCLEIC ACID INTERACTIONS : PROCEEDINGS OF THE FOURTH ANNUAL HARRY STEENBOCK SYMPOSIUM, JUNE 16-19, 1974, MADISON, WISCONSIN --: 431
    • The Binding of Riboflavin-5-Phosphate in a Flavoprotein. Flavodoxin at 2.0-Angstroms Resolution
      Watenpaugh, K.D.,Sieker, L.C.,Jensen, L.H.
      (1973) Proc.Natl.Acad.Sci.USA 70: 3857


    Organizational Affiliation

    Physical and Analytical Chemistry, Research Upjohn Co., Kalamazoo, MI 49007.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FLAVODOXIN
A
147Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Find proteins for P00323 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P00323
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download SDF File 
Download CCD File 
A
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 50.720α = 90.00
b = 50.720β = 90.00
c = 139.040γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other