Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 65.85 kDa 
• Atom Count: 5289 
• Modelled Residue Count: 574 
• Deposited Residue Count: 574 
• Unique protein chains: 1

1FEH

FE-ONLY HYDROGENASE FROM CLOSTRIDIUM PASTEURIANUM

• PDB DOI: 10.2210/pdb1FEH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Clostridium pasteurianum
• Mutation(s): No 


• Deposited: 1998-10-28 Released: 1999-01-13 
• Deposition Author(s): Peters, J.W., Lanzilotta, W.N., Lemon, B.J., Seefeldt, L.C.

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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 

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

• PubMed: 9836629 
• 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 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.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (PERIPLASMIC HYDROGENASE 1)	A	574	Clostridium pasteurianum	Mutation(s): 0  EC: 1.18.99.1 (PDB Primary Data), 1.12.7.2 (UniProt)
UniProt
Find proteins for P29166 (Clostridium pasteurianum) Explore P29166  Go to UniProtKB:  P29166

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HC1	B [auth A]	2 IRON/2 SULFUR/5 CARBONYL/2 WATER INORGANIC CLUSTER C5 H8 Fe2 O7 S2 DXKOXSKJHMBSFW-WPRITKAGAV
SF4	C [auth A], D [auth A], E [auth A], F [auth A]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-VKOJMFJBAC
FES	G [auth A]	FE2/S2 (INORGANIC) CLUSTER Fe2 S2 NIXDOXVAJZFRNF-UHFFFAOYSA-N

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 = 111.6	α = 90
b = 111.6	β = 90
c = 103.8	γ = 90

Software Package:

Software Name	Purpose
MADSYS	phasing
SOLVE	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-10-28 
• Released Date: 1999-01-13 
Deposition Author(s): Peters, J.W., Lanzilotta, W.N., Lemon, B.J., Seefeldt, L.C.

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