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: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

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This is version 1.3 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 7: 549-556

  • DOI: https://doi.org/10.1016/s0969-2126(99)80071-9
  • Primary Citation of Related Structures:  
    1H2R

  • 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 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.

    • Organizational Affiliation: 

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


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT)A [auth S]267Nitratidesulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
EC: 1.12.2.1
UniProt
Find proteins for P21853 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21853 
Go to UniProtKB:  P21853
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21853
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT)B [auth L]534Nitratidesulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
EC: 1.12.2.1
UniProt
Find proteins for P21852 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21852 
Go to UniProtKB:  P21852
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21852
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File 
C [auth S],
D [auth S]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
F3S
Query on F3S
Download Ideal Coordinates CCD File 
E [auth S]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-UHFFFAOYSA-N
NFE
Query on NFE
Download Ideal Coordinates CCD File 
G [auth L]NI-FE ACTIVE CENTER
C2 H Fe Ni O3 S2
BWHVFYQLNHWUMU-UHFFFAOYSA-M
MG
Query on MG
Download Ideal Coordinates CCD File 
F [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.44α = 90
b = 126.86β = 90
c = 66.68γ = 90
Software Package:
Software NamePurpose
PROTEINmodel building
MLPHAREphasing
X-PLORrefinement
DENZOdata reduction
CCP4data scaling
PROTEINphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-01-05
    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: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description