1NFV Iron Storage Electron Transport date Dec 16, 2002
title X-Ray Structure Of Desulfovibrio Desulfuricans Bacterioferri Diiron Centre In Different Catalytic States (As-Isolated St
authors S.Macedo, C.V.Romao, E.Mitchell, P.M.Matias, M.Y.Liu, A.V.Xavier, M.Teixeira, P.Lindley, M.A.Carrondo
compound source
Molecule: Bacterioferritin
Chain: A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
 Organism_scientific: Desulfovibrio Desulfuricans
Organism_taxid: 876
Strain: Atcc 27774
symmetry Space Group: P 21 3
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
225.300 225.300 225.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.95 Å
ligand 3PY, FE, FEC, GOL, SO4 enzyme
related structures by homologous chain: 1NF4
Gene
Ontology
ChainFunctionProcessComponent
F, N, K, E, M, C, L, A, J, O, P, B, H, D, I, G


Primary referenceThe nature of the di-iron site in the bacterioferritin from Desulfovibrio desulfuricans., Macedo S, Romao CV, Mitchell E, Matias PM, Liu MY, Xavier AV, LeGall J, Teixeira M, Lindley P, Carrondo MA, Nat Struct Biol 2003 Apr;10(4):285-90. PMID:12627224
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (520 Kb) [Save to disk]
  • Biological Unit Coordinates (1nfv.pdb1.gz) 501 Kb
  • Biological Unit Coordinates (1nfv.pdb2.gz) 744 Kb
  • Biological Unit Coordinates (1nfv.pdb3.gz) 750 Kb
  • LPC: Ligand-Protein Contacts for 1NFV
  • CSU: Contacts of Structural Units for 1NFV
  • Likely Quarternary Molecular Structure file(s) for 1NFV
  • Structure Factors (2638 Kb)
  • Retrieve 1NFV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NFV from S2C, [Save to disk]
  • Re-refined 1nfv structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1NFV 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 1NFV
  • 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 1NFV, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nfva_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nfvb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1nfvc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nfvd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1nfve_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1nfvf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1nfvg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1nfvh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1nfvi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1nfvj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1nfvk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1nfvl_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1nfvm_, region M [Jmol] [rasmolscript] [script source]
        - Domain d1nfvn_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1nfvo_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1nfvp_, region P [Jmol] [rasmolscript] [script source]
  • 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: [1nfv_M] [1nfv_B] [1nfv_H] [1nfv_L] [1nfv_A] [1nfv_E] [1nfv_O] [1nfv_G] [1nfv_F] [1nfv_P] [1nfv_I] [1nfv_K] [1nfv_C] [1nfv] [1nfv_N] [1nfv_J] [1nfv_D]
  • SWISS-PROT database: [Q93PP9]
  • Domain organization of [BFR_DESDA] by SWISSPFAM
    • Other resources with information on 1NFV
  • Community annotation for 1NFV 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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