2JIO Oxidoreductase date Jun 28, 2007
title A New Catalytic Mechanism Of Periplasmic Nitrate Reductase F Desulfovibrio Desulfuricans Atcc 27774 From Crystallographi Data And Based On Detailed Analysis Of The Sixth Ligand
authors S.Najmudin, P.J.Gonzalez, J.Trincao, C.Coelho, A.Mukhopadhyay, C. I.Moura, J.J.G.Moura, C.D.Brondino, M.J.Romao
compound source
Molecule: Periplasmic Nitrate Reductase
Chain: A
Ec: 1.7.99.4
 Organism_scientific: Desulfovibrio Desulfuricans
Organism_taxid: 876
Atcc: 27774
symmetry Space Group: P 31 2 1
R_factor 0.150 R_Free 0.209
crystal
cell
length a length b length c angle alpha angle beta angle gamma
106.188 106.188 135.130 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand MGD, MO, SF4, UNX enzyme Oxidoreductase E.C.1.7.99.4 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A
  • electron transfer activity


    • Primary referencePeriplasmic nitrate reductase revisited: a sulfur atom completes the sixth coordination of the catalytic molybdenum., Najmudin S, Gonzalez PJ, Trincao J, Coelho C, Mukhopadhyay A, Cerqueira NM, Romao CC, Moura I, Moura JJ, Brondino CD, Romao MJ, J Biol Inorg Chem. 2008 Mar 8;. PMID:18327621
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (137 Kb) [Save to disk]
  • Biological Unit Coordinates (2jio.pdb1.gz) 130 Kb
  • LPC: Ligand-Protein Contacts for 2JIO
  • CSU: Contacts of Structural Units for 2JIO
  • Likely Quarternary Molecular Structure file(s) for 2JIO
  • Structure Factors (332 Kb)
  • Retrieve 2JIO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2JIO from S2C, [Save to disk]
  • Re-refined 2jio structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2JIO 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 2JIO
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2JIO, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2jio_A] [2jio]
  • SWISS-PROT database: [P81186]
  • Domain organization of [NAPA_DESDA] by SWISSPFAM
  • Domain found in 2JIO: [Molybdop_Fe4S4 ] by SMART
    • Other resources with information on 2JIO
  • Community annotation for 2JIO at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
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  • Images from IMB Jena Image Library of Biological Macromolecules.

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