1CC1

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.8 of the entry. See complete history


Literature

The crystal structure of a reduced [NiFeSe] hydrogenase provides an image of the activated catalytic center

Garcin, E.Vernede, X.Hatchikian, E.C.Volbeda, A.Frey, M.Fontecilla-Camps, J.C.

(1999) Structure 7: 557-566

  • DOI: https://doi.org/10.1016/s0969-2126(99)80072-0
  • Primary Citation of Related Structures:  
    1CC1

  • PubMed Abstract: 

    [NiFeSe] hydrogenases are metalloenzymes that catalyze the reaction H2<-->2H+ + 2e-. They are generally heterodimeric, contain three iron-sulfur clusters in their small subunit and a nickel-iron-containing active site in their large subunit that includes a selenocysteine (SeCys) ligand.


  • Organizational Affiliation

    Institut de Biologie Structurale JP Ebel, Laboratoire de Cristallographie et Cristallogénèse des Protéines, CEA-CNRS, Grenoble, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HYDROGENASE (SMALL SUBUNIT)A [auth S]283Desulfomicrobium baculatumMutation(s): 0 
EC: 1.18.99.1
UniProt
Find proteins for P13063 (Desulfomicrobium baculatum)
Explore P13063 
Go to UniProtKB:  P13063
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13063
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HYDROGENASE (LARGE SUBUNIT)B [auth L]498Desulfomicrobium baculatumMutation(s): 0 
EC: 1.18.99.1
UniProt
Find proteins for P13065 (Desulfomicrobium baculatum)
Explore P13065 
Go to UniProtKB:  P13065
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13065
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.194 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.39α = 90
b = 63.7β = 90
c = 99.58γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
CCP4data reduction
AMoREphasing
X-PLORrefinement
XDSdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-06-01
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2014-02-19
    Changes: Atomic model, Structure summary
  • Version 1.4: 2014-08-06
    Changes: Derived calculations, Structure summary
  • Version 1.5: 2018-04-04
    Changes: Data collection
  • Version 1.6: 2018-04-11
    Changes: Data collection
  • Version 1.7: 2019-11-20
    Changes: Database references, Derived calculations
  • Version 1.8: 2023-08-09
    Changes: Data collection, Database references, Derived calculations, Refinement description