Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6107.46 
• Atom Count: 433 
• Residue Count: 54 
• Unique protein chains: 1

1IRO

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

• DOI: 10.2210/pdb1IRO/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Clostridium pasteurianum


• Deposited: 1995-12-13 Released: 1996-04-03 
• Deposition Author(s): Dauter, Z., Wilson, K.S., Sieker, L.C., Moulis, J.M., Meyer, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å

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.USA 93: 8836-8840

• PubMed: 8799113 
• Primary Citation of Related Structures:  
  1IRN


• 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 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.

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Related Citations: 

• 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
• 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.,Sect.B 29: 943




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
RUBREDOXIN	A	54	Clostridium pasteurianum	Mutation(s): 0
Find proteins for P00268 (Clostridium pasteurianum) Go to UniProtKB:  P00268

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
FE	A	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.1 Å
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 64.040	α = 90.00
b = 64.040	β = 90.00
c = 32.510	γ = 120.00

Software Package:

Software Name	Purpose
SHELXL-93	phasing
ARP	model building
SHELXL-93	model building
SHELXL-93	refinement
SCALEPACK	data scaling
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1995-12-13 
• Released Date: 1996-04-03 
• Deposition Author(s): Dauter, Z., Wilson, K.S., Sieker, L.C., Moulis, J.M., Meyer, J.

Revision History 

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