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 1.7 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: 10.1016/s0969-2126(99)80072-0
  • Structures With Same Primary Citation

  • 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 incl ...

    [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.


    Related Citations: 
    • Structure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands
      Volbeda, A., Garcin, E., Piras, C., De Lacey, A.L., Fernandez, V.M., Hatchikian, E.C., Frey, M., Fontecilla-Camps, J.C.
      (1996) J Am Chem Soc 118: 12989

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE (SMALL SUBUNIT)
S
283Desulfomicrobium baculatumMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.99.6 (UniProt)
Find proteins for P13063 (Desulfomicrobium baculatum)
Go to UniProtKB:  P13063
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HYDROGENASE (LARGE SUBUNIT)
L
498Desulfomicrobium baculatumMutation(s): 0 
EC: 1.18.99.1 (PDB Primary Data), 1.12.99.6 (UniProt)
Find proteins for P13065 (Desulfomicrobium baculatum)
Go to UniProtKB:  P13065
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

Download CCD File 
L
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download CCD File 
L
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
FE2
Query on FE2

Download CCD File 
L
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

Download CCD File 
L
HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
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 

  • 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