2RDV

RUBREDOXIN FROM DESULFOVIBRIO VULGARIS MIYAZAKI F, MONOCLINIC CRYSTAL FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure determination of rubredoxin from Desulfovibrio vulgaris Miyazaki F in two crystal forms.

Misaki, S.Morimoto, Y.Ogata, M.Yagi, T.Higuchi, Y.Yasuoka, N.

(1999) Acta Crystallogr.,Sect.D 55: 408-413

  • DOI: 10.1107/s0907444998011810
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replaceme ...

    The structures of two crystal forms (form I, P3221, a = b = 43.7, c = 50.7 A; form II, P21, a = 27.3, b = 44.9, c = 51.2 A and beta = 90. 6 degrees ) of the rubredoxin from Desulfovibrio vulgaris Miyazaki F have been solved by the molecular-replacement method. Form I has been refined at a resolution of 2.0 A to an R value of 20.8% and includes 32 water molecules. Form II includes 86 water molecules and has been refined at 1.9 A resolution to an R value of 17.5%. In form II, there are three molecules in the asymmetric unit with the molecules related by a non-crystallographic 32 symmetry axis. In both crystal forms, it was found that only a few residues effectively participate in the formation of intermolecular contacts along both the crystallographic (form I) and the non-crystallographic (form II) 32 axes. The crystal structure of the form II crystal is compared with those of other rubredoxin molecules from anaerobic bacteria. From this comparison, a similarity in the core region, which is composed of aromatic residues and includes the active centre, has been revealed.


    Related Citations: 
    • Preliminary Crystallographic Study of Two Crystal Forms of Rubredoxin from Sulfate-Reducing Bactrium
      Higuchi, Y.,Sugiyama, M.S.,Morimoto, S.,Ogata, Y.,Yagi, M.,Yasuoka, T.
      (1998) Protein Pept.Lett. 5: 175


    Organizational Affiliation

    Department of Life Science, Faculty of Science, Himeji Institute of Technology, Kanaji 1475-2, Kamigori, Ako-gun, Hyogo 678-1297, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBREDOXIN
A, B, C
52Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Mutation(s): 0 
Gene Names: rub
Find proteins for P15412 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P15412
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download SDF File 
Download CCD File 
A, B, C
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 27.300α = 90.00
b = 44.900β = 90.60
c = 51.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
FSCALEdata scaling
X-PLORphasing
WEISdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-18
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance