3SSR | pdb_00003ssr

CcmK2 dodecamer - form 2

PDB DOI: https://doi.org/10.2210/pdb3SSR/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Thermosynechococcus vestitus BP-1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.178 (Depositor), 0.167 (DCC)
R-Value Work:
0.153 (Depositor), 0.151 (DCC)
R-Value Observed:
0.155 (Depositor)

Starting Model: experimental
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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: 24.08 kDa
Atom Count: 1,645
Modeled Residue Count: 198
Deposited Residue Count: 220
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon dioxide concentrating mechanism protein	A [auth B], B [auth A]	110	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.178 (Depositor), 0.167 (DCC)
R-Value Work: 0.153 (Depositor), 0.151 (DCC)
R-Value Observed: 0.155 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.05	α = 90
b = 74.05	β = 90
c = 66.4	γ = 120

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-07-11

Deposition Author(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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.