1FRV

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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

  • DOI: 10.1038/373580a0
  • Also Cited By: 1YQ9

  • 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 s ...

    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.


    Related Citations: 
    • Location of the Redox Centers in Hydrogenase as Determined by X-Ray Crystallography at 5 Angstroms Resolution
      Volbeda, A.,Piras, C.,Charon, M.H.,Hatchikian, E.C.,Frey, M.,Fontecilla-Camps, J.C.
      (1993) Joint Ccp4 Esf-Eacbm Newsletter on Protein Crystallography 28: 30
    • Analysis and Comparison of Nucleotide Sequences Encoding the Genes for [Nife] and [Nifese] Hydrogenases from Desulfovibrio Gigas and Desulfovibrio Baculatus
      Voordouw, G.,Menon, N.K.,Legall, J.,Choi, E.S.,Peck Junior, H.D.,Przybyla, A.E.
      (1989) J.Bacteriol. 171: 2894


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE
A, C
264Desulfovibrio gigasGene Names: hydA
EC: 1.12.2.1
Find proteins for P12943 (Desulfovibrio gigas)
Go to UniProtKB:  P12943
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE
B, D
536Desulfovibrio gigasGene Names: hydB
EC: 1.12.2.1
Find proteins for P12944 (Desulfovibrio gigas)
Go to UniProtKB:  P12944
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download SDF File 
Download CCD File 
A, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download SDF File 
Download CCD File 
A, C
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
FEL
Query on FEL

Download SDF File 
Download CCD File 
B, D
HYDRATED FE
Fe H6 O3
MSNWSDPPULHLDL-BKVXGLREAH
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
B, D
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 63.600α = 89.80
b = 93.900β = 102.90
c = 69.200γ = 90.80
Software Package:
Software NamePurpose
MOSFLMdata reduction
PROLSQrefinement
SCALKB/KBAPLYdata reduction
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
BIOMOLdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance