3SSQ | pdb_00003ssq

CcmK2 - form 1 dodecamer

• PDB DOI: https://doi.org/10.2210/pdb3SSQ/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Thermosynechococcus vestitus BP-1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-07-08 Released: 2012-07-11 
• Deposition Author(s): Samborska, B., Kimber, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Starting Model: experimental

Literature

A CcmK2 double layer is the dominant architectural feature of the beta-carboxysomal shell facet

Samborska, B., Kimber, M.S.

(2012) Structure 

Biological Assembly 1  

Global Symmetry: Dihedral - D6  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.78 kDa 
• Atom Count: 4,751 
• Modeled Residue Count: 602 
• Deposited Residue Count: 732 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon dioxide concentrating mechanism protein	A, B, C, D, E, F	122	Thermosynechococcus vestitus BP-1	Mutation(s): 0  Gene Names: ccmK2, tll0947
UniProt
Find proteins for Q8DKB2 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DKB2  Go to UniProtKB:  Q8DKB2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	G [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	H [auth B], I [auth E], J [auth F], K [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.187 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.362	α = 90
b = 83.362	β = 90
c = 226.86	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-07-11 
Deposition Author(s): Samborska, B., Kimber, M.S.

Revision History  

• Version 1.0: 2012-07-11
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description