1FEH

FE-ONLY HYDROGENASE FROM CLOSTRIDIUM PASTEURIANUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution.

Peters, J.W.Lanzilotta, W.N.Lemon, B.J.Seefeldt, L.C.

(1998) Science 282: 1853-1858

  • DOI: 10.1126/science.282.5395.1853
  • Primary Citation of Related Structures:  
    1FEH

  • PubMed Abstract: 
  • A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzym ...

    A three-dimensional structure for the monomeric iron-containing hydrogenase (CpI) from Clostridium pasteurianum was determined to 1.8 angstrom resolution by x-ray crystallography using multiwavelength anomalous dispersion (MAD) phasing. CpI, an enzyme that catalyzes the two-electron reduction of two protons to yield dihydrogen, was found to contain 20 gram atoms of iron per mole of protein, arranged into five distinct [Fe-S] clusters. The probable active-site cluster, previously termed the H-cluster, was found to be an unexpected arrangement of six iron atoms existing as a [4Fe-4S] cubane subcluster covalently bridged by a cysteinate thiol to a [2Fe] subcluster. The iron atoms of the [2Fe] subcluster both exist with an octahedral coordination geometry and are bridged to each other by three non-protein atoms, assigned as two sulfide atoms and one carbonyl or cyanide molecule. This structure provides insights into the mechanism of biological hydrogen activation and has broader implications for [Fe-S] cluster structure and function in biological systems.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA. petersj@cc.usu.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (PERIPLASMIC HYDROGENASE 1)A574Clostridium pasteurianumMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.7.2 (UniProt)
Find proteins for P29166 (Clostridium pasteurianum)
Explore P29166 
Go to UniProtKB:  P29166
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HC1
Query on HC1

Download CCD File 
A
2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER
C5 H8 Fe2 O7 S2
DXKOXSKJHMBSFW-WPRITKAGAV
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FES
Query on FES

Download CCD File 
A
FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.180 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.6α = 90
b = 111.6β = 90
c = 103.8γ = 90
Software Package:
Software NamePurpose
MADSYSphasing
SOLVEphasing
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance