1E2U

Low Temperature Structure of Hybrid Cluster Protein from Desulfovibrio vulgaris to 1.6A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Hybrid-Cluster Protein (Hcp) from Desulfovibrio Vulgaris (Hildenborough) at 1.6 A Resolution.

Cooper, S.J.Garner, C.D.Hagen, W.R.Lindley, P.F.Bailey, S.

(2000) Biochemistry 39: 15044

  • Primary Citation of Related Structures:  1E1D

  • PubMed Abstract: 
  • The three-dimensional structure of the hybrid cluster protein from Desulfovibrio vulgaris (Hildenborough) has been determined at 1.6 A resolution using synchrotron X-ray radiation. The protein can be divided into three domains: an N-terminal mainly a ...

    The three-dimensional structure of the hybrid cluster protein from Desulfovibrio vulgaris (Hildenborough) has been determined at 1.6 A resolution using synchrotron X-ray radiation. The protein can be divided into three domains: an N-terminal mainly alpha-helical domain and two similar domains comprising a central beta-sheet flanked by alpha-helices. The protein contains two 4Fe clusters with an edge-to-edge distance of 10.9 A. Four cysteine residues at the N-terminus of the protein are ligands to the iron atoms of a conventional [4Fe-4S] cubane cluster. The second cluster has an unusual asymmetric structure and has been named the hybrid cluster to reflect the variety of protein ligands, namely two mu-sulfido bridges, two mu(2)-oxo bridges, and a further disordered bridging ligand. Anomalous differences in data collected at 1.488 A and close to the iron edge at 1.743 A have been used to confirm the identity of the metal and sulfur atoms. The hybrid cluster is buried in the center of the protein, but is accessible through a large hydrophobic cavity that runs the length of domain 3. Hydrophobic channels have previously been identified as access routes to the active centers in redox enzymes with gaseous substrates. The hybrid cluster is also accessible by a hydrophilic channel. The [4Fe-4S] cubane cluster is close to an indentation on the surface of the protein and can also be approached on the opposite side by a long solvent channel. At the present time, neither the significance of these channels nor, indeed, the function of the hybrid cluster protein is known.


    Organizational Affiliation

    School of Chemistry, Nottingham University, University Park, Nottingham, NG7 2RD, U.K.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROXYLAMINE REDUCTASE
A
553Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303)Gene Names: hcp
EC: 1.7.99.1
Find proteins for P31101 (Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / NCIMB 8303))
Go to UniProtKB:  P31101
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FSO
Query on FSO

Download SDF File 
Download CCD File 
A
IRON/SULFUR/OXYGEN HYBRID CLUSTER
Fe4 O3 S3
NIIPGMCXXHQOSA-LVFFOBLJCB
 Ligand Interaction
SF4
Query on SF4

Download SDF File 
Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSS
Query on CSS
A
L-PEPTIDE LINKINGC3 H7 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.184 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 63.630α = 90.00
b = 64.680β = 90.00
c = 152.290γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-12-11
    Type: Initial release
  • Version 1.1: 2012-11-28
    Type: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2013-04-24
    Type: Structure summary