2D2C Photosynthesis date Sep 07, 2005
title Crystal Structure Of Cytochrome B6f Complex With Dbmib From Laminosus
authors J.Yan, G.Kurisu, W.A.Cramer
compound source
Molecule: Cytochrome B6
Chain: A, N
 Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Cytochrome B6-F Complex Subunit 4
Chain: B, O
Synonym: 17 Kda Polypeptide
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Apocytochrome F
Chain: C, P
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Cytochrome B6-F Complex Iron-Sulfur Subunit
Chain: D, Q
Synonym: Rieske Iron-Sulfur Protein, Plastohydroquinone:Pla Oxidoreductase Iron-Sulfur Protein, Isp, Risp;
Ec: 1.10.99.1
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Cytochrome B6-F Complex Subunit Vi
Chain: E, R
Synonym: Cytochrome B6f Complex Subunit Petl
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Cytochrome B6-F Complex Subunit Vii
Chain: F, S
Synonym: Cytochrome B6f Complex Subunit Petm
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Cytochrome B6-F Complex Subunit V
Chain: G, T
Synonym: Cytochrome B6f Complex Subunit Petg
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541

Molecule: Cytochrome B6-F Complex Subunit Viii
Chain: H, U
Synonym: Cytochrome B6f Complex Subunit Petn
Organism_scientific: Mastigocladus Laminosus
Organism_taxid: 83541
symmetry Space Group: P 61
R_factor 0.276 R_Free 0.378
crystal
cell
length a length b length c angle alpha angle beta angle gamma
156.587 156.587 361.786 90.00 90.00 120.00
method X-Ray Diffractionresolution 3.80 Å
ligand BCR, BNT, CLA, FES, HEC, HEM, OPC enzyme Oxidoreductase E.C.1.10.99.1 BRENDA
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 referenceIntraprotein transfer of the quinone analogue inhibitor 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone in the cytochrome b6f complex., Yan J, Kurisu G, Cramer WA, Proc Natl Acad Sci U S A. 2006 Jan 3;103(1):69-74. Epub 2005 Dec 21. PMID:16371475
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (296 Kb) [Save to disk]
  • Biological Unit Coordinates (2d2c.pdb1.gz) 283 Kb
  • LPC: Ligand-Protein Contacts for 2D2C
  • CSU: Contacts of Structural Units for 2D2C
  • Likely Quarternary Molecular Structure file(s) for 2D2C
  • Structure Factors (421 Kb)
  • Retrieve 2D2C in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2D2C from S2C, [Save to disk]
  • Re-refined 2d2c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2D2C 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 2D2C
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 2D2C, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2d2c_G] [2d2c_A] [2d2c_R] [2d2c_Q] [2d2c_F] [2d2c_N] [2d2c_O] [2d2c_B] [2d2c] [2d2c_C] [2d2c_P] [2d2c_D] [2d2c_U] [2d2c_S] [2d2c_E] [2d2c_T] [2d2c_H]
  • 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 2D2C
  • Community annotation for 2D2C 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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