1HPI

MOLECULAR STRUCTURE OF THE OXIDIZED HIGH-POTENTIAL IRON-SULFUR PROTEIN ISOLATED FROM ECTOTHIORHODOSPIRA VACUOLATA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular structure of the oxidized high-potential iron-sulfur protein isolated from Ectothiorhodospira vacuolata.

Benning, M.M.Meyer, T.E.Rayment, I.Holden, H.M.

(1994) Biochemistry 33: 2476-2483

  • DOI: https://doi.org/10.1021/bi00175a016
  • Primary Citation of Related Structures:  
    1HPI

  • PubMed Abstract: 

    The high-potential iron-sulfur protein (iso-form II) isolated from Ectothiorhodospira vacuolata has been crystallized and its three-dimensional structure determined by molecular replacement procedures and refined to 1.8-A resolution with a crystallographic R factor of 16.3%. Crystals employed in the investigation belonged to the space group C222(1) with unit cell dimensions of a = 58.4 A, b = 64.7 A, and c = 39.3 A and one molecule per asymmetric unit. Like those HiPIPs structurally characterized thus far, the E. vacuolata molecule contains mostly reverse turns that wrap around the iron-sulfur cluster with cysteine residues 34, 37, 51, and 65 ligating the metal center to the polypeptide chain. There are 57 ordered solvent molecules, most of which lie at the surface of the protein. Two of these water molecules play important structural roles by stabilizing the loops located between Asp 42 and Lys 57. The metal center binding pocket is decidedly hydrophobic with the closest solvent molecule being 6.9 A from S2 of the [4Fe-4S] cluster. The E. vacuolata HiPIP molecules pack in the crystalline lattice as dimers with their iron-sulfur centers approximately 17.5 A apart. On the basis of biochemical properties, it was anticipated that the E. vacuolata HiPIP would be structurally more similar to the HiPIP isolated from Ectothiorhodospira halophila than to the protein obtained from Chromatium vinosum. In fact, the E. vacuolata molecule is as structurally close to the C. vinosum HiPIP as it is to the E. halophila protein due to the presence of various insertions and deletions that disrupt local folding.(ABSTRACT TRUNCATED AT 250 WORDS)


  • Organizational Affiliation

    Institute for Enzyme Research, Graduate School, University of Wisconsin, Madison 53705.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIGH POTENTIAL IRON SULFUR PROTEIN71Ectothiorhodospira shaposhnikoviiMutation(s): 0 
UniProt
Find proteins for P38524 (Ectothiorhodospira shaposhnikovii)
Explore P38524 
Go to UniProtKB:  P38524
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38524
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
B [auth A]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.163 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.4α = 90
b = 64.7β = 90
c = 39.3γ = 90
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1994-04-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations