1FRV | pdb_00001frv

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

PDB DOI: https://doi.org/10.2210/pdb1FRV/pdb

Classification: OXIDOREDUCTASE
Organism(s): Megalodesulfovibrio gigas
Mutation(s): No

Deposited: 1996-03-28 Released: 1996-11-08
Deposition Author(s): Volbeda, A., Frey, M., Fontecilla-Camps, J.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas.

Volbeda, A., Charon, M.H., Piras, C., Hatchikian, E.C., Frey, M., Fontecilla-Camps, J.C.

(1995) Nature 373: 580-587

PubMed: 7854413 Search on PubMed
DOI: https://doi.org/10.1038/373580a0
Primary Citation Related Structures:
1FRV

PubMed Abstract:
The X-ray structure of the heterodimeric Ni-Fe hydrogenase from Desulfovibrio gigas, the enzyme responsible for the metabolism of molecular hydrogen, has been solved at 2.85 A resolution. The active site, which appears to contain, besides nickel, a second metal ion, is buried in the 60K subunit. The 28K subunit, which coordinates one [3Fe-4S] and two [4Fe-4S] clusters, contains an amino-terminal domain with similarities to the redox protein flavodoxin. The structure suggests plausible electron and proton transfer pathways.

Organizational Affiliation

Laboratoire de Cristallographie et de Cristallogénèse des Protéines, Institut de Biologie Structurale J. P. Ebel (CEA, CNRS), Grenoble, France.

Macromolecule Content

Total Structure Weight: 178.83 kDa
Atom Count: 12,268
Modeled Residue Count: 1,584
Deposited Residue Count: 1,600
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE	A, C	264	Megalodesulfovibrio gigas	Mutation(s): 0 EC: 1.12.2.1
UniProt
Find proteins for P12943 (Megalodesulfovibrio gigas) Explore P12943 Go to UniProtKB: P12943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12943
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HYDROGENASE	B, D	536	Megalodesulfovibrio gigas	Mutation(s): 0 EC: 1.12.2.1
UniProt
Find proteins for P12944 (Megalodesulfovibrio gigas) Explore P12944 Go to UniProtKB: P12944
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12944
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain J [auth C] SDF format, chain G [auth A] SDF format, chain E [auth A] MOL2 format, chain L [auth C] MOL2 format, chain J [auth C] MOL2 format, chain G [auth A] MOL2 format, chain E [auth A] mmCIF format, chain L [auth C] mmCIF format, chain J [auth C] mmCIF format, chain G [auth A] mmCIF format, chain E [auth A]	E [auth A], G [auth A], J [auth C], L [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain L [auth C]
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain K [auth C] SDF format, chain F [auth A] MOL2 format, chain K [auth C] MOL2 format, chain F [auth A] mmCIF format, chain K [auth C] mmCIF format, chain F [auth A]	F [auth A], K [auth C]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth C]
FEL Query on FEL Download:Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain I [auth B] MOL2 format, chain N [auth D] MOL2 format, chain I [auth B] mmCIF format, chain N [auth D] mmCIF format, chain I [auth B]	I [auth B], N [auth D]	HYDRATED FE Fe H₆ O₃ MSNWSDPPULHLDL-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Focus chain N [auth D]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain H [auth B] MOL2 format, chain M [auth D] MOL2 format, chain H [auth B] mmCIF format, chain M [auth D] mmCIF format, chain H [auth B]	H [auth B], M [auth D]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain M [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.6	α = 89.8
b = 93.9	β = 102.9
c = 69.2	γ = 90.8

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALKB/KBAPLY	data reduction
X-PLOR	model building
PROLSQ	refinement
X-PLOR	refinement
BIOMOL	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 1996-11-08

Deposition Author(s):

Volbeda, A.

Frey, M.

Fontecilla-Camps, J.C.

Revision History (Full details and data files)

Version 1.0: 1996-11-08
Type: Initial release
Version 1.1: 2008-03-03
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-10-23
Changes: Data collection, Database references, Derived calculations, Structure summary