8RXN

REFINEMENT OF RUBREDOXIN FROM DESULFOVIBRIO VULGARIS AT 1.0 ANGSTROMS WITH AND WITHOUT RESTRAINTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 A with and without restraints.

Dauter, Z.Sieker, L.C.Wilson, K.S.

(1992) Acta Crystallogr.,Sect.B 48: 42-59


  • PubMed Abstract: 
  • X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging ...

    X-ray data have been recorded from crystals of rubredoxin derived from the bacterium Desulfovibrio vulgaris to a resolution of 1.0 A using in part synchrotron radiation and in part X-rays from a sealed-tube Mo K alpha source. In both cases an imaging-plate scanner was used as detector. The space group of the crystals is P2(1) with cell dimensions a = 19.97, b = 41.45, c = 24.41 A and beta = 108.3 degrees. The overall merging R(I) factor between symmetry-related reflections was 5.8%. The model was refined by least-squares minimization initially with stereochemical restraints to an R factor of 16.4%. Only atomic positional parameters and isotropic temperature factors for non-H atoms were used in the refinement. There were 18,532 independent X-ray observations for a total of 1916 atomic parameters. A round of unrestrained refinement gave an R factor of 16.0%, acceptable geometry for more than 90% of the protein atoms, but emphasized the disorder inherent in eight of the residues. A final round of restrained refinement gave an R factor of 14.7%. Three of the 389 protein atoms in the molecule, in the side chain of Lys2, have been assigned zero occupancy in the model. A total of eight atoms in three side chains have been assigned two conformations, giving 393 protein atomic sites in the model. In addition there is one Fe atom, a sulfate ion and 102 water sites. 339 H atoms were included at their calculated positions, which were not refined. There is clear evidence for anisotropic thermal motion. This has not been incorporated in the present model.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Hamburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RUBREDOXIN
A
52Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303)Mutation(s): 0 
Gene Names: rub
Find proteins for P00269 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / DSM 644 / NCIMB 8303))
Go to UniProtKB:  P00269
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
FE
Query on FE

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 19.970α = 90.00
b = 41.450β = 108.30
c = 24.410γ = 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: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance