1WUK

High resolution Structure Of The Oxidized State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.094 
  • R-Value Observed: 0.096 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Activation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state

Ogata, H.Hirota, S.Nakahara, A.Komori, H.Shibata, N.Kato, T.Kano, K.Higuchi, Y.

(2005) Structure 13: 1635-1642

  • DOI: 10.1016/j.str.2005.07.018
  • Primary Citation of Related Structures:  
    1WUL, 1WUK, 1WUJ, 1WUI

  • PubMed Abstract: 
  • Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready) ...

    Hydrogenases catalyze oxidoreduction of molecular hydrogen and have potential applications for utilizing dihydrogen as an energy source. [NiFe] hydrogenase has two different oxidized states, Ni-A (unready, exhibits a lag phase in reductive activation) and Ni-B (ready). We have succeeded in converting Ni-B to Ni-A with the use of Na2S and O2 and determining the high-resolution crystal structures of both states. Ni-B possesses a monatomic nonprotein bridging ligand at the Ni-Fe active site, whereas Ni-A has a diatomic species. The terminal atom of the bridging species of Ni-A occupies a similar position as C of the exogenous CO in the CO complex (inhibited state). The common features of the enzyme structures at the unready (Ni-A) and inhibited (CO complex) states are proposed. These findings provide useful information on the design of new systems of biomimetic dihydrogen production and fuel cell devices.


    Organizational Affiliation

    Department of Life Science, Graduate School of Life Science, University of Hyogo and Himeji Institute of Technology, 3-2-1 Koto, Ako-gun, Hyogo 678-1297, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunitA [auth S]267Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydADvMF_0271
EC: 1.12.2.1
UniProt
Find proteins for P21853 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21853 
Go to UniProtKB:  P21853
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunitB [auth L]534Desulfovibrio vulgaris str. 'Miyazaki FMutation(s): 0 
Gene Names: hydBDvMF_0270
EC: 1.12.2.1
UniProt
Find proteins for P21852 (Desulfovibrio vulgaris (strain DSM 19637 / Miyazaki F))
Explore P21852 
Go to UniProtKB:  P21852
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / 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-VKOJMFJBAC
 Ligand Interaction
F3S
Query on F3S

Download Ideal Coordinates CCD File 
E [auth S]FE3-S4 CLUSTER
Fe3 S4
FCXHZBQOKRZXKS-MZMDZPPWAW
 Ligand Interaction
NFO (Subject of Investigation/LOI)
Query on NFO

Download Ideal Coordinates CCD File 
H [auth L]NI-FE OXIDIZED ACTIVE CENTER
C3 H2 Fe N Ni O3
FQZPNHHVQDQMNS-UHFFFAOYSA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
F [auth S](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
B [auth L]L-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 0.123 
  • R-Value Work: 0.094 
  • R-Value Observed: 0.096 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.291α = 90
b = 125.843β = 90
c = 66.44γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-09-04
    Changes: Atomic model, Data collection, Derived calculations