4KO2 | pdb_00004ko2

Low X-ray dose structure of H2-activated anaerobically purified Dm. baculatum [NiFeSe]-hydrogenase after crystallization under air

Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.60 Å
  • R-Value Free:&nbsp
    0.194 (Depositor), 0.194 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.162 (Depositor), 0.163 (DCC)&nbsp
  • R-Value Observed:&nbsp
    0.164&nbsp(Depositor)&nbsp

Starting Model: experimental
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wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 2.2 of the entry. See complete&nbsphistory.&nbsp


Literature

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

Volbeda, A.,&nbspAmara, P.,&nbspIannello, M.,&nbspDe Lacey, A.L.,&nbspCavazza, C.,&nbspFontecilla-Camps, J.C.

(2013) Chem Commun (Camb)&nbsp49: 7061-7063

  • DOI:&nbsphttps://doi.org/10.1039/c3cc43619e
  • Primary Citation of Related Structures: &nbsp
    4KL8, 4KN9, 4KO1, 4KO2, 4KO3, 4KO4

  • PubMed Abstract:&nbsp

    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.

    • Organizational Affiliation:&nbsp

    Metalloproteins Unit, Institut de Biologie Structurale J.P. Ebel, CEA, CNRS, Université Grenoble Alpes UMR 5075, 41 rue Jules Horowitz, 38027 Grenoble, France. [email protected]


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Periplasmic [NiFeSe] hydrogenase small subunitA [auth S],
C [auth T]		283Desulfomicrobium baculatumMutation(s): 0&nbsp
EC:&nbsp1.12.99.6
UniProt
Find proteins for&nbspP13063&nbsp(Desulfomicrobium baculatum)
Explore&nbspP13063&nbsp
Go to UniProtKB: &nbspP13063
Entity Groups &nbsp
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
Nickel-dependent hydrogenase large subunitB [auth L],
D [auth M]		499Desulfomicrobium baculatum DSM 4028Mutation(s): 0&nbsp
EC:&nbsp1.18.99.1
UniProt
Find proteins for&nbspC7LN88&nbsp(Desulfomicrobium baculatum (strain DSM 4028 / VKM B-1378 / X))
Explore&nbspC7LN88&nbsp
Go to UniProtKB: &nbspC7LN88
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupC7LN88
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands&nbsp6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SF4
Query on SF4
Download Ideal Coordinates CCD File&nbsp
E [auth S]
F [auth S]
G [auth S]
Q [auth T]
R [auth T]
E [auth S],
F [auth S],
G [auth S],
Q [auth T],
R [auth T],
S [auth T]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
FCO
Query on FCO
Download Ideal Coordinates CCD File&nbsp
M [auth L],
W [auth M]		CARBONMONOXIDE-(DICYANO) IRON
C3 Fe N2 O
VBQUCMTXYFMTTE-UHFFFAOYSA-N
GOL
Query on GOL
Download Ideal Coordinates CCD File&nbsp
AA [auth M],
BA [auth M],
I [auth S],
J [auth S]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI
Query on NI
Download Ideal Coordinates CCD File&nbsp
N [auth L],
X [auth M]		NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
CA
Query on CA
Download Ideal Coordinates CCD File&nbsp
H [auth S]
K [auth S]
L [auth S]
O [auth L]
T
H [auth S],
K [auth S],
L [auth S],
O [auth L],
T,
U [auth T],
V [auth T],
Y [auth M]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
H2S
Query on H2S
Download Ideal Coordinates CCD File&nbsp
P [auth L],
Z [auth M]		HYDROSULFURIC ACID
H2 S
RWSOTUBLDIXVET-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D 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 H6 N O3 SeSEC
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp1.60 Å
  • R-Value Free:&nbsp 0.194 (Depositor), 0.194 (DCC)&nbsp
  • R-Value Work:&nbsp 0.162 (Depositor), 0.163 (DCC)&nbsp
  • R-Value Observed:&nbsp0.164&nbsp(Depositor)&nbsp
Space Group:&nbspP 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.23α = 90
b = 108.91β = 90
c = 136.34γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
REFMACrefinement
XDSdata reduction

Structure Validation

View&nbspFull Validation Report



View more in-depth experimental data
Entry History&nbsp

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: 2016-06-15
    Changes: Non-polymer description
  • Version 1.7: 2017-11-15
    Changes: Refinement description
  • Version 1.8: 2019-05-08
    Changes: Advisory, Data collection, Database references
  • Version 2.0: 2022-10-26
    Changes: Database references, Derived calculations, Non-polymer description
  • Version 2.1: 2023-09-20
    Changes: Data collection, Refinement description
  • Version 2.2: 2024-11-27
    Changes: Structure summary