4JVZ

Structure of Thermosynechococcus elongatus CcmL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Two new high-resolution crystal structures of carboxysome pentamer proteins reveal high structural conservation of CcmL orthologs among distantly related cyanobacterial species.

Sutter, M.Wilson, S.C.Deutsch, S.Kerfeld, C.A.

(2013) Photosynth Res 118: 9-16

  • DOI: https://doi.org/10.1007/s11120-013-9909-z
  • Primary Citation of Related Structures:  
    4JVZ, 4JW0

  • PubMed Abstract: 

    Cyanobacteria have evolved a unique carbon fixation organelle known as the carboxysome that compartmentalizes the enzymes RuBisCO and carbonic anhydrase. This effectively increases the local CO2 concentration at the active site of RuBisCO and decreases its relatively unproductive side reaction with oxygen. Carboxysomes consist of a protein shell composed of hexameric and pentameric proteins arranged in icosahedral symmetry. Facets composed of hexameric proteins are connected at the vertices by pentameric proteins. Structurally homologous pentamers and hexamers are also found in heterotrophic bacteria where they form architecturally related microcompartments such as the Eut and Pdu organelles for the metabolism of ethanolamine and propanediol, respectively. Here we describe two new high-resolution structures of the pentameric shell protein CcmL from the cyanobacteria Thermosynechococcus elongatus and Gloeobacter violaceus and provide detailed analysis of their characteristics and comparison with related shell proteins.


  • Organizational Affiliation

    United States Department of Energy - Joint Genome Institute, Walnut Creek, CA, 94598, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Carbon dioxide concentrating mechanism protein
A, B, C, D, E
99Thermosynechococcus vestitus BP-1Mutation(s): 0 
Gene Names: ccmL
UniProt
Find proteins for Q8DKB4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DKB4 
Go to UniProtKB:  Q8DKB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DKB4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.249 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.445α = 90
b = 72.445β = 90
c = 197.449γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AutoSolphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-09-04
    Type: Initial release
  • Version 1.1: 2013-11-27
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations