2FRV Oxidoreductase date Jun 10, 1997
title Crystal Structure Of The Oxidized Form Of Ni-Fe Hydrogenase
authors A.Volbeda, M.Frey, J.C.Fontecilla-Camps
compound source
Molecule: Periplasmic Hydrogenase
Chain: S, A, C, E, G, I
Synonym: Cytochrome-C3 Hydrogenase
Ec: 1.18.99.1
Organism_scientific: Desulfovibrio Gigas
Organism_taxid: 879
Collection: Atcc 19364
Cellular_location: Periplasm

Molecule: Periplasmic Hydrogenase
Chain: L, B, D, F, H, J
Synonym: Cytochrome-C3 Hydrogenase
Ec: 1.18.99.1

Organism_scientific: Desulfovibrio Gigas
Organism_taxid: 879
Collection: Atcc 19364
Cellular_location: Periplasm
symmetry Space Group: P 1
R_factor 0.201 R_Free 0.219
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.780 113.160 133.910 90.03 90.02 119.99
method X-Ray Diffractionresolution 2.54 Å
ligand F3S, FCO, MG, NI, O, SF4 enzyme Oxidoreductase E.C.1.18.99.1 BRENDA
note 2FRV (Molecule of the Month:pdb111)
related structures by homologous chain: 1FRF, 1YQ9
Gene
Ontology
ChainFunctionProcessComponent
F, J, B, H, D, L


S, A, E, C, I, G


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (758 Kb) [Save to disk]
  • Biological Unit Coordinates (2frv.pdb1.gz) 136 Kb
  • Biological Unit Coordinates (2frv.pdb2.gz) 134 Kb
  • Biological Unit Coordinates (2frv.pdb3.gz) 135 Kb
  • Biological Unit Coordinates (2frv.pdb4.gz) 135 Kb
  • Biological Unit Coordinates (2frv.pdb5.gz) 136 Kb
  • Biological Unit Coordinates (2frv.pdb6.gz) 135 Kb
  • LPC: Ligand-Protein Contacts for 2FRV
  • CSU: Contacts of Structural Units for 2FRV
  • Likely Quarternary Molecular Structure file(s) for 2FRV
  • Retrieve 2FRV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2FRV from S2C, [Save to disk]
  • View 2FRV in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 2FRV
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2FRV, from MSDmotif at EBI
  • Genome occurence of 2FRV's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d2frva_, region A [Jmol] [rasmolscript] [script source]
        - Domain d2frvb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d2frvc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d2frvd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d2frve_, region E [Jmol] [rasmolscript] [script source]
        - Domain d2frvf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d2frvg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d2frvh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d2frvi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d2frvj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d2frvl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d2frvs_, region S [Jmol] [rasmolscript] [script source]
  • Fold representative 2frv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2frv] [2frv_G] [2frv_H] [2frv_E] [2frv_A] [2frv_S] [2frv_L] [2frv_F] [2frv_I] [2frv_C] [2frv_D] [2frv_J] [2frv_B]
  • SWISS-PROT database: [P12944] [P12943]
  • Domain organization of [PHNL_DESGI] [PHNS_DESGI] by SWISSPFAM
  • Other resources with information on 2FRV
  • Community annotation for 2FRV at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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