4KO3

Low X-ray dose structure of anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural foundations for the O2 resistance of Desulfomicrobium baculatum [NiFeSe]-hydrogenase.

Volbeda, A.Amara, P.Iannello, M.De Lacey, A.L.Cavazza, C.Fontecilla-Camps, J.C.

(2013) Chem.Commun.(Camb.) 49: 7061-7063

  • DOI: 10.1039/c3cc43619e
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • This study shows how the NiFeSe site of an anaerobically purified O2-resistant hydrogenase reacts with air to give a seleninate as the first product. Less oxidized states of the active site are readily reduced in the presence of X-rays. Reductive enz ...

    This study shows how the NiFeSe site of an anaerobically purified O2-resistant hydrogenase reacts with air to give a seleninate as the first product. Less oxidized states of the active site are readily reduced in the presence of X-rays. Reductive enzyme activation requires an efficient pathway for water escape.


    Related Citations: 
    • 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


    Organizational Affiliation

    Metalloproteins Unit, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Grenoble Alpes UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France. anne.volbeda@ibs.fr




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Periplasmic [NiFeSe] hydrogenase small subunit
S, T
283Desulfomicrobium baculatumMutation(s): 0 
EC: 1.12.99.6
Find proteins for P13063 (Desulfomicrobium baculatum)
Go to UniProtKB:  P13063
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nickel-dependent hydrogenase large subunit
L, M
499Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378)Mutation(s): 0 
Find proteins for C7LN88 (Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378))
Go to UniProtKB:  C7LN88
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

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

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Download CCD File 
L, M
CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
H2S
Query on H2S

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Download CCD File 
L, M
HYDROSULFURIC ACID
HYDROGEN SULFIDE
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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S
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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M, S
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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L, M, S, T
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

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L, M
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UOX
Query on UOX
L, M
L-PEPTIDE LINKINGC3 H7 N O3 SeSEC
SE7
Query on SE7
L, M
L-PEPTIDE LINKINGC3 H7 N O4 SeSEC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 106.200α = 90.00
b = 108.720β = 90.00
c = 136.620γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
MxCuBEdata collection
XDSdata reduction
REFMACrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Database references
  • Version 1.2: 2013-07-24
    Type: Database references
  • Version 1.3: 2013-12-25
    Type: Other
  • Version 1.4: 2014-04-09
    Type: Other
  • Version 1.5: 2016-06-08
    Type: Atomic model
  • Version 2.0: 2019-05-08
    Type: Advisory, Data collection, Derived calculations, Polymer sequence