Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C6  (3D View)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.58 kDa 
• Atom Count: 1441 
• Modelled Residue Count: 182 
• Deposited Residue Count: 198 
• Unique protein chains: 1

4LIW

CcmK1 Carboxysome Shell Protein from Synechocystis PCC6803, L11K Point Mutant

• PDB DOI: 10.2210/pdb4LIW/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Synechocystis sp. PCC 6803 substr. Kazusa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-07-03 Released: 2014-01-08 
• Deposition Author(s): Thompson, M.C., Yeates, T.O.

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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 

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

• PubMed: 24419393 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon dioxide-concentrating mechanism protein CcmK homolog 1	A, B	99	Synechocystis sp. PCC 6803 substr. Kazusa	Mutation(s): 1  Gene Names: ccmK1, sll1029
UniProt
Find proteins for P72760 (Synechocystis sp. (strain PCC 6803 / Kazusa)) Explore P72760  Go to UniProtKB:  P72760

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

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 = 70.02	α = 90
b = 70.02	β = 90
c = 56.25	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-03 
• Released Date: 2014-01-08 
Deposition Author(s): Thompson, M.C., Yeates, T.O.

Revision History  

• 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