ISDA: 4KO3

Deposition Date 2013-05-11

Release Date 2013-07-10

Last Version Date 2023-09-20

Entry Detail

PDB ID:

4KO3

Keywords:

OXIDOREDUCTASE

Title:

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

Biological Source:

Source Organism:

Desulfomicrobium baculatum (Taxon ID: 899)
Desulfomicrobium baculatum (Taxon ID: 525897)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.70 Å

R-Value Free:

0.20

R-Value Work:

0.16

R-Value Observed:

0.16

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Nickel-dependent hydrogenase large subunit
Gene (Uniprot):Dbac_1969
Chain IDs:B (auth: L), D (auth: M)
Chain Length:499
Number of Molecules:2
Biological Source:Desulfomicrobium baculatum

UniProt ID:C7LN88 Pfam ID:PF00374

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Periplasmic [NiFeSe] hydrogenase small subunit
Chain IDs:A (auth: S), C (auth: T)
Chain Length:283
Number of Molecules:2
Biological Source:Desulfomicrobium baculatum

UniProt ID:P13063 Pfam ID:PF01058, PF14720

Modified Residue

Compound ID	Chain ID	Parent Comp ID	Details	2D Image
SE7	B	ALA	2-AMINO-3-SELENINO-PROPIONIC ACID
UOX	B	SEC	3-(OXIDO-LAMBDA~4~-SELANYL)-L-ALANINE

Ligand Molecules

FCO

GOL

H2S

SF4

Primary Citation

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

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

PMID: 23811828 DOI: 10.1039/c3cc43619e

Abstact

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.

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Primary Citation of related structures