1WUI

Ultra-High resolution Structure Of The Ni-A State Of [Nife]Hydrogenase From Desulufovibrio Vulgaris Miyazaki F


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.04 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.098 

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

  • 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). 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase small subunitA [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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [NiFe] hydrogenase large subunitB [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 6 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
NFC
Query on NFC

Download Ideal Coordinates CCD File 
J [auth L]NI-FE ACTIVE CENTER A-FORM
C3 H2 Fe N Ni O4
CIUCFLVMTAQNSJ-UHFFFAOYSA-N
MRD
Query on MRD

Download Ideal Coordinates CCD File 
K [auth L](4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth S],
G [auth S],
H [auth S]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
I [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D 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: 1.04 Å
  • R-Value Free: 0.134 
  • R-Value Work: 0.096 
  • R-Value Observed: 0.098 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.069α = 90
b = 125.966β = 90
c = 66.38γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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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