1IRO

RUBREDOXIN (OXIDIZED, FE(III)) AT 1.1 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Observed: 0.090 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Zinc- and iron-rubredoxins from Clostridium pasteurianum at atomic resolution: a high-precision model of a ZnS4 coordination unit in a protein.

Dauter, Z.Wilson, K.S.Sieker, L.C.Moulis, J.M.Meyer, J.

(1996) Proc Natl Acad Sci U S A 93: 8836-8840

  • DOI: 10.1073/pnas.93.17.8836
  • Primary Citation of Related Structures:  
    1IRN, 1IRO

  • PubMed Abstract: 
  • The Zn(Scys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A ...

    The Zn(Scys)4 unit is present in numerous proteins, where it assumes structural, regulatory, or catalytic roles. The same coordination is found naturally around iron in rubredoxins, several structures of which have been refined at resolutions of, or near to, 1 A. The fold of the small protein rubredoxin around its metal ion is an excellent model for many zinc finger proteins. Zn-substituted rubredoxin and its Fe-containing counterpart were both obtained as the products of the expression in Escherichia coli of the rubredoxin-encoding gene from Clostridium pasteurianum. The structures of both proteins have been refined with an anisotropic model at atomic resolution (1.1 A, R = 8.3% for Fe-rubredoxin, and 1.2 A, R = 9.6% for Zn-rubredoxin) and are very similar. The most significant differences are increased lengths of the M-S bonds in Zn-rubredoxin (average length, 2.345 A) as compared with Fe-rubredoxin (average length, 2.262 A). An increase of the CA-CB-SG-M dihedral angles involving Cys-6 and Cys-39, the first cysteines of each of the Cys-Xaa-Xaa-Cys metal binding motifs, has been observed. Another consequence of the replacement of iron by zinc is that the region around residues 36-46 undergoes larger displacements than the remainder of the polypeptide chain. Despite these changes, the main features of the FeS4 site, namely a local 2-fold symmetry and the characteristic network of N-H...S hydrogen bonds, are conserved in the ZnS4 site. The Zn-substituted rubredoxin provides the first precise structure of a Zn(Scys)4 unit in a protein. The nearly identical fold of rubredoxin around iron or zinc suggests that at least in some of the sites where the metal has mainly a structural role-e.g., zinc fingers-the choice of the relevant metal may be directed by its cellular availability and mobilization processes rather than by its chemical nature.


    Related Citations: 
    • Crystallographic Refinement of Rubredoxin at 1.2 Angstroms Resolution
      Watenpaugh, K.D., Sieker, L.C., Jensen, L.H.
      (1980) J Mol Biol 138: 615
    • Refinement of the Model of a Protein. Rubredoxin at 1.5 Angstroms Resolution
      Watenpaugh, K.D., Sieker, L.C., Herriott, J.R., Jensen, L.H.
      (1973) Acta Crystallogr B 29: 943
    • Structure of Rubredoxin. An X-Ray Study to 2.5 Angstroms Resolution
      Herriott, J.R., Sieker, L.C., Jensen, L.H., Lovenberg, W.
      (1970) J Mol Biol 50: 391

    Organizational Affiliation

    European Molecular Biology Laboratory, Deutsches Elektronen Synchrotron, Hamburg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RUBREDOXINA54Clostridium pasteurianumMutation(s): 0 
UniProt
Find proteins for P00268 (Clostridium pasteurianum)
Explore P00268 
Go to UniProtKB:  P00268
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00268
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE
Query on FE

Download Ideal Coordinates CCD File 
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Observed: 0.090 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.04α = 90
b = 64.04β = 90
c = 32.51γ = 120
Software Package:
Software NamePurpose
SHELXL-93model building
SHELXL-93refinement
ARPmodel building
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-93phasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance