4LIW

CcmK1 Carboxysome Shell Protein from Synechocystis PCC6803, L11K Point Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A challenging interpretation of a hexagonally layered protein structure.

Thompson, M.C.Yeates, T.O.

(2014) Acta Crystallogr D Biol Crystallogr 70: 203-208

  • DOI: 10.1107/S139900471302422X
  • Primary Citation of Related Structures:  
    4LIW

  • PubMed Abstract: 
  • The carboxysome is a giant protein complex that acts as a metabolic organelle in cyanobacteria and some chemoautotrophs. Its outer structure is formed by the assembly of thousands of copies of hexameric shell protein subunits into a molecular layer. The structure determination of a CcmK1 shell protein mutant (L11K) from the β-carboxysome of the cyanobacterium Synechocystis PCC6803 led to challenges in structure determination ...

    The carboxysome is a giant protein complex that acts as a metabolic organelle in cyanobacteria and some chemoautotrophs. Its outer structure is formed by the assembly of thousands of copies of hexameric shell protein subunits into a molecular layer. The structure determination of a CcmK1 shell protein mutant (L11K) from the β-carboxysome of the cyanobacterium Synechocystis PCC6803 led to challenges in structure determination. Twinning, noncrystallographic symmetry and packing of hexameric units in a special arrangement led to initial difficulties in space-group assignment. The correct space group was clarified after initial model refinement revealed additional symmetry. This study provides an instructive example in which broken symmetry requires a new choice of unit-cell origin in order to identify the highest symmetry space group. An additional observation related to the packing arrangement of molecules in this crystal suggests that these hexameric shell proteins might have lower internal symmetry than previously believed.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, UCLA, Los Angeles, CA 90095, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carbon dioxide-concentrating mechanism protein CcmK homolog 1A, B99Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 1 
Gene Names: ccmK1sll1029
UniProt
Find proteins for P72760 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P72760 
Go to UniProtKB:  P72760
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72760
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.192 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.02α = 90
b = 70.02β = 90
c = 56.25γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-01-08
    Type: Initial release
  • Version 1.1: 2014-02-12
    Changes: Database references
  • Version 1.2: 2018-04-04
    Changes: Data collection, Source and taxonomy