1H2A

SINGLE CRYSTALS OF HYDROGENASE FROM DESULFOVIBRIO VULGARIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 1671-1680

  • DOI: 10.1016/s0969-2126(97)00313-4
  • Primary Citation of Related Structures:  
    1H2A

  • PubMed Abstract: 
  • The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure ...

    The hydrogenase of Desulfovibrio sp. catalyzes the reversible oxidoreduction of molecular hydrogen, in conjunction with a specific electron acceptor, cytochrome c3. The Ni-Fe active center of Desulfovibrio hydrogenase has an unusual ligand structure with non-protein ligands. An atomic model at high resolution is required to make concrete assignment of the ligands which coordinate the Ni-Fe center. These in turn will provide insight into the mechanism of electron transfer, during the reaction catalysed by hydrogenase.


    Related Citations: 
    • Location of Active Sites of Nife Hydrogenase Determined by the Combination of Multiple Isomorphous Replacement and Multiwavelength Anomalous-Diffraction Methods
      Higuchi, Y., Okamoto, T., Fujimoto, K., Misaki, S., Morimoto, Y., Yasouka, N.
      (1994) Acta Crystallogr D Biol Crystallogr 50: 781
    • Single Crystals of Hydrogenase from Desulfovibrio Vulgaris Miyazaki F
      Higuchi, Y., Yasuoka, N., Kakudo, M., Katsube, Y., Yagi, T., Inokuchi, H.
      (1987) J Biol Chem 262: 2823

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROGENASES317Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydADvMF_0271
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
Find proteins for P21853 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Explore P21853 
Go to UniProtKB:  P21853
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HYDROGENASEL567Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydBDvMF_0270
EC: 1.18.99.1 (PDB Primary Data), 1.12.2.1 (UniProt)
Find proteins for P21852 (Desulfovibrio vulgaris (strain Miyazaki F / DSM 19637))
Explore P21852 
Go to UniProtKB:  P21852
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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

Download CCD File 
L
NI-FE ACTIVE CENTER
C2 H Fe Ni O3 S2
BWHVFYQLNHWUMU-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
L
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.229 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.5α = 90
b = 126.5β = 90
c = 66.51γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
FSCALEdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-02-09
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance