4KO4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.7 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:  
    4KL8, 4KO1, 4KO2, 4KO3, 4KO4, 4KN9

  • 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 enzyme activation requires an efficient pathway for water escape ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase small subunitA [auth S], C [auth T]283Desulfomicrobium baculatumMutation(s): 0 
EC: 1.12.99.6
UniProt
Find proteins for P13063 (Desulfomicrobium baculatum)
Explore P13063 
Go to UniProtKB:  P13063
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nickel-dependent hydrogenase large subunitB [auth L], D [auth M]499Desulfomicrobium baculatum DSM 4028Mutation(s): 0 
Gene Names: Dbac_1969
EC: 1.18.99.1
UniProt
Find proteins for C7LN88 (Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378 / X))
Explore C7LN88 
Go to UniProtKB:  C7LN88
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4

Download Ideal Coordinates CCD File 
E [auth S], F [auth S], G [auth S], Q [auth T], R [auth T], S [auth T]IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
FCO
Query on FCO

Download Ideal Coordinates CCD File 
M [auth L], W [auth M]CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
AA [auth M], BA [auth M], J [auth S], K [auth S]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download Ideal Coordinates CCD File 
N [auth L], X [auth M]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
CA [auth M], H [auth S], L [auth S], O [auth L], T, U [auth T], V [auth T], Y [auth M]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
I [auth S]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
H2S
Query on H2S

Download Ideal Coordinates CCD File 
P [auth L], Z [auth M]HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
SE7
Query on SE7
B [auth L], D [auth M]L-PEPTIDE LINKINGC3 H7 N O4 SeSEC
UOX
Query on UOX
B [auth L], D [auth M]L-PEPTIDE LINKINGC3 H7 N O3 SeSEC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.2α = 90
b = 108.72β = 90
c = 136.62γ = 90
Software Package:
Software NamePurpose
Xnemodata collection
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-10
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references
  • Version 1.3: 2013-12-25
    Changes: Other
  • Version 1.4: 2014-04-09
    Changes: Other
  • Version 1.5: 2014-08-06
    Changes: Other
  • Version 1.6: 2016-06-08
    Changes: Atomic model
  • Version 1.7: 2019-05-08
    Changes: Advisory, Data collection