1HFE

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

• PDB DOI: https://doi.org/10.2210/pdb1HFE/pdb

• Classification: HYDROGENASE
• Organism(s): Nitratidesulfovibrio vulgaris str. Hildenborough
• Mutation(s): No 


• Deposited: 1998-11-11 Released: 1999-04-20 
• Deposition Author(s): Nicolet, Y., Piras, C., Legrand, P., Hatchikian, E.C., Fontecilla-Camps, J.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.182 
• R-Value Work: 0.158 

Literature

Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center.

Nicolet, Y., Piras, C., Legrand, P., Hatchikian, C.E., Fontecilla-Camps, J.C.

(1999) Structure 7: 13-23

• PubMed: 10368269 
• DOI: https://doi.org/10.1016/s0969-2126(99)80005-7
• Primary Citation of Related Structures:  
  1HFE


• PubMed Abstract: 
  

  Many microorganisms have the ability to either oxidize molecular hydrogen to generate reducing power or to produce hydrogen in order to remove low-potential electrons. These reactions are catalyzed by two unrelated enzymes: the Ni-Fe hydrogenases and the Fe-only hydrogenases.

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Organizational Affiliation: 

Laboratoire de Cristallographie et de Cristallogènese des Protéines, Institut de Biologie Structurale Jean-Pierre Ebel, CEA-CNRS 41, 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)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 122.39 kDa 
• Atom Count: 9,079 
• Modelled Residue Count: 970 
• Deposited Residue Count: 1,088 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))	A [auth S], C [auth T]	123	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  EC: 1.18.99.1
UniProt
Find proteins for P07603 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07603  Go to UniProtKB:  P07603

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER SUBUNIT))	B [auth L], D [auth M]	421	Nitratidesulfovibrio vulgaris str. Hildenborough	Mutation(s): 0  EC: 1.18.99.1
UniProt
Find proteins for P07598 (Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough)) Explore P07598  Go to UniProtKB:  P07598

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SF4	J [auth L], K [auth L], L, U [auth M], V [auth M], W [auth M]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
CYS	AA [auth M], P [auth L]	CYSTEINE C3 H7 N O2 S XUJNEKJLAYXESH-REOHCLBHSA-N
PDT	M [auth L], X [auth M]	1,3-PROPANEDITHIOL C3 H8 S2 ZJLMKPKYJBQJNH-UHFFFAOYSA-N
ZN	E [auth S]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
FE2	F [auth L], G [auth L], Q [auth M], R [auth M]	FE (II) ION Fe CWYNVVGOOAEACU-UHFFFAOYSA-N
CMO	N [auth L], O [auth L], Y [auth M], Z [auth M]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N
CYN	H [auth L], I [auth L], S [auth M], T [auth M]	CYANIDE ION C N XFXPMWWXUTWYJX-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.182 
• R-Value Work: 0.158 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.97	α = 90
b = 123.07	β = 90
c = 65.07	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-20 
Deposition Author(s): Nicolet, Y., Piras, C., Legrand, P., Hatchikian, E.C., Fontecilla-Camps, J.C.

Revision History  

• Version 1.0: 1999-04-20
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-11-20
  Changes: Advisory, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Advisory, Data collection, Database references, Derived calculations