1H2R

THREE-DIMENSIONAL STRUCTURE OF NI-FE HYDROGENASE FROM DESULFIVIBRIO VULGARIS MIYAZAKI F IN THE REDUCED FORM AT 1.4 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Removal of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.

Higuchi, Y.Ogata, H.Miki, K.Yasuoka, N.Yagi, T.

(1999) Structure Fold.Des. 7: 549-556


  • PubMed Abstract: 
  • The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two o ...

    The active site of [NiFe] hydrogenase, a heterodimeric protein, is suggested to be a binuclear Ni-Fe complex having three diatomic ligands to the Fe atom and three bridging ligands between the Fe and Ni atoms in the oxidized form of the enzyme. Two of the bridging ligands are thiolate sidechains of cysteinyl residues of the large subunit, but the third bridging ligand was assigned as a non-protein monatomic sulfur species in Desulfovibrio vulgaris Miyazaki F hydrogenase.


    Related Citations: 
    • Unusual Ligand Structure in Ni-Fe Active Center and an Additional Mg Site in Hydrogenase Revealed by High Resolution X-Ray Structure Analysis
      Higuchi, Y.,Yagi, T.,Yasuoka, N.
      (1997) Structure 5: 1671
    • Liberation of Hydrogen Sulfide During the Catalytic Action of Desulfoviborio Hydrogenase Under the Atmosphere of Hydrogen
      Higuchi, Y.,Yagi, T.
      (1999) Biochem.Biophys.Res.Commun. 255: 295


    Organizational Affiliation

    Division of Chemistry, Graduate School of Science, Kyoto University, Japan. higuchi@kuchem.kyoto-u.ac.jp




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT)
S
267Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Gene Names: hydA
EC: 1.12.2.1
Find proteins for P21853 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21853
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT)
L
534Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637)Gene Names: hydB
EC: 1.12.2.1
Find proteins for P21852 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Go to UniProtKB:  P21852
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

Download SDF File 
Download CCD File 
S
FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NFE
Query on NFE

Download SDF File 
Download CCD File 
L
NI-FE ACTIVE CENTER
C2 H Fe Ni O3 S2
BWHVFYQLNHWUMU-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.440α = 90.00
b = 126.860β = 90.00
c = 66.680γ = 90.00
Software Package:
Software NamePurpose
MLPHAREphasing
PROTEINphasing
X-PLORrefinement
CCP4data scaling
DENZOdata reduction
PROTEINmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1999-06-14 
  • Released Date: 2000-01-05 
  • Deposition Author(s): Higuchi, Y., Ogata, H.

Revision History 

  • Version 1.0: 2000-01-05
    Type: Initial release
  • Version 1.1: 2008-04-26
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance