1VF5 Photosynthesis date Apr 08, 2004
title Crystal Structure Of Cytochrome B6f Complex From M.Laminosus
authors G.Kurisu, H.Zhang, J.L.Smith, W.A.Cramer
compound source
Molecule: Cytochrome B6
Chain: A, N
 Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Subunit Iv
Chain: B, O
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Cytochrome F
Chain: C, P
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Rieske Iron-Sulfur Protein
Chain: D, Q
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Protein Pet L
Chain: E, R
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Protein Pet M
Chain: F, S
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Protein Pet G
Chain: G, T
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium

Molecule: Protein Pet N
Chain: H, U
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
Other_details: Thermophilic Cyanobacterium
symmetry Space Group: P 61
R_factor 0.258 R_Free 0.346
crystal
cell
length a length b length c angle alpha angle beta angle gamma
157.536 157.536 360.347 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.00 Å
ligand BCR, CLA, FES, HEM, OPC, PL9, TDS enzyme
note 1VF5 (Molecule of the Month:pdb137)is a representative structure and supersedes 1UM3
related structures by homologous chain: 1CI3, 1RFS, 1TU2
Gene
Ontology
ChainFunctionProcessComponent
A, N


E, R
  • electron transfer activity
  • electron transporter, transf...


    • H, U
  • electron transfer activity
  • electron transporter, transf...


    • O, B


    P, C
  • electron transfer activity


    • Q, D
  • electron transporter, transf...


    • S, F
  • electron transfer activity


    • T, G
  • electron transporter, transf...


    • Primary referenceStructure of the cytochrome b6f complex of oxygenic photosynthesis: tuning the cavity., Kurisu G, Zhang H, Smith JL, Cramer WA, Science 2003 Nov 7;302(5647):1009-14. Epub 2003 Oct 2. PMID:14526088
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (295 Kb) [Save to disk]
  • Biological Unit Coordinates (1vf5.pdb1.gz) 281 Kb
  • LPC: Ligand-Protein Contacts for 1VF5
  • CSU: Contacts of Structural Units for 1VF5
  • Likely Quarternary Molecular Structure file(s) for 1VF5
  • Structure Factors (831 Kb)
  • Retrieve 1VF5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VF5 from S2C, [Save to disk]
  • Re-refined 1vf5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1VF5 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 1VF5
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VF5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vf5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1vf5b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1vf5c1, region C:1-169,C:232-249 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5c2, region C:170-231 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5c3, region C:250-286 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5d2, region D:12-45 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5d1, region D:46-179 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5e_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1vf5f_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1vf5g_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1vf5h_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1vf5n_, region N [Jmol] [rasmolscript] [script source]
        - Domain d1vf5o_, region O [Jmol] [rasmolscript] [script source]
        - Domain d1vf5p1, region P:1-169,P:232-249 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5p2, region P:170-231 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5p3, region P:250-286 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5q2, region Q:12-45 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5q1, region Q:46-179 [Jmol] [rasmolscript] [script source]
        - Domain d1vf5r_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1vf5s_, region S [Jmol] [rasmolscript] [script source]
        - Domain d1vf5t_, region T [Jmol] [rasmolscript] [script source]
        - Domain d1vf5u_, region U [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: [1vf5_E] [1vf5_S] [1vf5_C] [1vf5_R] [1vf5_N] [1vf5_F] [1vf5_A] [1vf5_B] [1vf5_H] [1vf5_D] [1vf5_O] [1vf5_T] [1vf5_Q] [1vf5_P] [1vf5_G] [1vf5] [1vf5_U]
  • SWISS-PROT database: [P83791] [P83793] [P83792] [P83797] [P83795] [P83796] [P83798] [P83794]
  • Domain organization of [CYB6_MASLA] [CYF_MASLA] [PETD_MASLA] [PETG_MASLA] [PETL_MASLA] [PETM_MASLA] [PETN_MASLA] [UCRI_MASLA] by SWISSPFAM
    • Other resources with information on 1VF5
  • Community annotation for 1VF5 at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science