1FRV

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

• PDB DOI: https://doi.org/10.2210/pdb1FRV/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Megalodesulfovibrio gigas
• Mutation(s): No 


• Deposited: 1996-03-28 Released: 1996-11-08 
• Deposition Author(s): Volbeda, A., Frey, M., Fontecilla-Camps, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å

Literature

Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas.

Volbeda, A., Charon, M.H., Piras, C., Hatchikian, E.C., Frey, M., Fontecilla-Camps, J.C.

(1995) Nature 373: 580-587

• PubMed: 7854413 
• DOI: https://doi.org/10.1038/373580a0
• Primary Citation of Related Structures:  
  1FRV


• PubMed Abstract: 
  

  The X-ray structure of the heterodimeric Ni-Fe hydrogenase from Desulfovibrio gigas, the enzyme responsible for the metabolism of molecular hydrogen, has been solved at 2.85 A resolution. The active site, which appears to contain, besides nickel, a second metal ion, is buried in the 60K subunit. The 28K subunit, which coordinates one [3Fe-4S] and two [4Fe-4S] clusters, contains an amino-terminal domain with similarities to the redox protein flavodoxin. The structure suggests plausible electron and proton transfer pathways.

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Organizational Affiliation: 

Laboratoire de Cristallographie et de Cristallogénèse des Protéines, Institut de Biologie Structurale J. P. Ebel (CEA, CNRS), Grenoble, France.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 178.83 kDa 
• Atom Count: 12,268 
• Modelled Residue Count: 1,584 
• Deposited Residue Count: 1,600 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE	A, C	264	Megalodesulfovibrio gigas	Mutation(s): 0  EC: 1.12.2.1
UniProt
Find proteins for P12943 (Megalodesulfovibrio gigas) Explore P12943  Go to UniProtKB:  P12943

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE	B, D	536	Megalodesulfovibrio gigas	Mutation(s): 0  EC: 1.12.2.1
UniProt
Find proteins for P12944 (Megalodesulfovibrio gigas) Explore P12944  Go to UniProtKB:  P12944

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	E [auth A], G [auth A], J [auth C], L [auth C]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S	F [auth A], K [auth C]	FE3-S4 CLUSTER Fe3 S4 FCXHZBQOKRZXKS-UHFFFAOYSA-N
FEL	I [auth B], N [auth D]	HYDRATED FE Fe H6 O3 MSNWSDPPULHLDL-UHFFFAOYSA-N
NI	H [auth B], M [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.6	α = 89.8
b = 93.9	β = 102.9
c = 69.2	γ = 90.8

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALKB/KBAPLY	data reduction
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
BIOMOL	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-11-08 
Deposition Author(s): Volbeda, A., Frey, M., Fontecilla-Camps, J.C.

Revision History  

• Version 1.0: 1996-11-08
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-23
  Changes: Data collection, Database references, Derived calculations, Structure summary