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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.237 (Depositor), 0.238 (DCC)
R-Value Work:
0.187 (Depositor), 0.192 (DCC)
R-Value Observed:
0.189 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

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

Samborska, B., Kimber, M.S.

(2012) Structure

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

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon dioxide concentrating mechanism protein	A, B, C, D, E 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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DKB2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth F] SDF format, chain J [auth F] SDF format, chain I [auth E] SDF format, chain H [auth B] MOL2 format, chain K [auth F] MOL2 format, chain J [auth F] MOL2 format, chain I [auth E] MOL2 format, chain H [auth B] mmCIF format, chain K [auth F] mmCIF format, chain J [auth F] mmCIF format, chain I [auth E] mmCIF format, chain H [auth B]	H [auth B], I [auth E], J [auth F], K [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth B] Focus chain I [auth E] Focus chain J [auth F] Focus chain K [auth F] Interactions & Density Focus chain H [auth B] Focus chain I [auth E] Focus chain J [auth F] Focus chain K [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.237 (Depositor), 0.238 (DCC)
R-Value Work: 0.187 (Depositor), 0.192 (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

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(s):

Samborska, B.

Kimber, M.S.

Revision History (Full details and data files)

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

3SSQ | pdb_00003ssq

CcmK2 - form 1 dodecamer

Literature

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

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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