3BN4 Structural Protein date Dec 13, 2007
title Carboxysome Subunit, Ccmk1
authors S.Tanaka, M.R.Sawaya, T.O.Yeates
compound source
Molecule: Carbon Dioxide-Concentrating Mechanism Protein Cc 1;
Chain: A, B, C, D, E, F
Engineered: Yes
Organism_scientific: Synechocystis Sp.
Organism_taxid: 1143
Gene: Ccmk1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)Gold
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet22b
symmetry Space Group: C 1 2 1
R_factor 0.203 R_Free 0.250
length a length b length c angle alpha angle beta angle gamma
120.900 69.770 78.010 90.00 94.61 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand SO4 enzyme
note 3BN4 (Molecule of the Month:pdb114)
Primary referenceAtomic-level models of the bacterial carboxysome shell., Tanaka S, Kerfeld CA, Sawaya MR, Cai F, Heinhorst S, Cannon GC, Yeates TO, Science. 2008 Feb 22;319(5866):1083-6. PMID:18292340
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (93 Kb) [Save to disk]
  • Biological Unit Coordinates (3bn4.pdb1.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 3BN4
  • CSU: Contacts of Structural Units for 3BN4
  • Likely Quarternary Molecular Structure file(s) for 3BN4
  • Structure Factors (592 Kb)
  • Retrieve 3BN4 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3BN4 from S2C, [Save to disk]
  • Re-refined 3bn4 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3BN4 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 3BN4
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3BN4, from MSDmotif at EBI
  • Fold representative 3bn4 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3bn4_C] [3bn4] [3bn4_F] [3bn4_D] [3bn4_E] [3bn4_A] [3bn4_B]
  • SWISS-PROT database: [P72760]
  • Domain organization of [CCMK1_SYNY3] by SWISSPFAM
  • Domain found in 3BN4: [BMC ] by SMART
  • Other resources with information on 3BN4
  • Community annotation for 3BN4 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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