3SSS | pdb_00003sss

CcmK1 with residues 103-113 deleted

PDB DOI: https://doi.org/10.2210/pdb3SSS/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): Kimber, M.S., Samborska, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free:
0.211 (Depositor), 0.206 (DCC)
R-Value Work:
0.163 (Depositor), 0.161 (DCC)
R-Value Observed:
0.165 (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: 72.06 kDa
Atom Count: 4,942
Modeled Residue Count: 623
Deposited Residue Count: 660
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, B, C, D, E A, B, C, D, E, F	110	Thermosynechococcus vestitus BP-1	Mutation(s): 0 Gene Names: ccmK1, tll0946
UniProt
Find proteins for Q8DKB3 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1)) Explore Q8DKB3 Go to UniProtKB: Q8DKB3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8DKB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth D] MOL2 format, chain G [auth D] mmCIF format, chain G [auth D]	G [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth D] Interactions & Density Focus chain G [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.211 (Depositor), 0.206 (DCC)
R-Value Work: 0.163 (Depositor), 0.161 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.4	α = 90
b = 78.6	β = 90
c = 110.8	γ = 90

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	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):

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.