PDB-3ssr: CcmK2 dodecamer - form 2

ID or keywords:

Entry

Database: PDB / ID: 3ssr

Title

CcmK2 dodecamer - form 2

Components

Carbon dioxide concentrating mechanism protein

Keywords

STRUCTURAL PROTEIN / Bacterial Microcompartment Fold / Shell forming / pore forming

Function / homology

Function and homology information

structural constituent of carboxysome shell /

carboxysome /

carbon fixation /

photosynthesis / identical protein binding
Similarity search - Function

Biological species

Thermosynechococcus elongatus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Kimber, M.S. / Samborska, B.

Citation

Journal: Structure / Year: 2012
Title: A CcmK2 double layer is the dominant architectural feature of the beta-carboxysomal shell facet
Authors: Samborska, B. / Kimber, M.S.

History

Deposition	Jul 8, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.2	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3ssr.cif.gz	91.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3ssr.ent.gz	71.7 KB	Display	PDB format
PDBx/mmJSON format	3ssr.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ss/3ssr ftp://data.pdbj.org/pub/pdb/validation_reports/ss/3ssr	HTTPS FTP

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Related structure data

Related structure data	3ssqSC 3sssC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3ssq-1 1n9s-d 2xqu-1 5yja-d 2xqt-1 6ull-1 2ixd-1 5djb-6 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#114 - Jun 2009 Vaults similarity (7) #165 - Sep 2013 Designed Protein Cages similarity (4)

Deposited unit

B: Carbon dioxide concentrating mechanism protein

A: Carbon dioxide concentrating mechanism protein

hetero molecules

24.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

B: Carbon dioxide concentrating mechanism protein

A: Carbon dioxide concentrating mechanism protein

hetero molecules

x 6

defined by author
144 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_765	-y+2,x-y+1,z	1
crystal symmetry operation	3_675	-x+y+1,-x+2,z	1
crystal symmetry operation	4_775	-x+2,-y+2,z	1
crystal symmetry operation	5_565	y,-x+y+1,z	1
crystal symmetry operation	6_655	x-y+1,x,z	1

Unit cell

Length a, b, c (Å)	74.050, 74.050, 66.400
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	168
Space group name H-M	P6

Components on special symmetry positions

ID	Model	Components
1	1	B-111- SO4
2	1	A-171- HOH

#1: Protein	Carbon dioxide concentrating mechanism protein Mass: 11990.664 Da / Num. of mol.: 2 / Fragment: CcmK2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: ccmK2, tll0947 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8DKB2
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.19 Å³/Da / Density % sol: 43.87 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.9 Details: 25% PEG 4000, 0.2 M (NH4)2SO4 and 15% glycerol , pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 1, 2011 Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97949 Å / Relative weight: 1
Reflection twin	Operator: h,-h-k,-l / Fraction: 0.184
Reflection	Resolution: 1.6→32 Å / Num. all: 27433 / Num. obs: 27433 / % possible obs: 99.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.6 % / R_sym value: 0.058 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.6→1.63 Å / Mean I/σ(I) obs: 5 / R_sym value: 0.364 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
MxDC		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6.4_486)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3SSQ

3ssq

Resolution: 1.6→29.483 Å / σ(F): 0 / Phase error: 23.41

	R_factor	Num. reflection	% reflection
R_free	0.1782	1358	5 %
R_work	0.1531	-	-
obs	0.1555	27163	99.2 %
all	-	28339	-

Solvent computation

Shrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 96.545 Å² / k_sol: 0.454 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.027 Å²	-0 Å²	0 Å²
2-	-	-2.027 Å²	-0 Å²
3-	-	-	4.054 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→29.483 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1480	0	5	106	1591

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	1568
X-RAY DIFFRACTION	f_angle_d	0.893	2144
X-RAY DIFFRACTION	f_dihedral_angle_d	12.984	586
X-RAY DIFFRACTION	f_chiral_restr	0.058	261
X-RAY DIFFRACTION	f_plane_restr	0.003	276

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6003-1.6643	0.303	152	0.2964	2875	X-RAY DIFFRACTION	95
1.6643-1.7401	0.2686	151	0.2506	2869	X-RAY DIFFRACTION	95
1.7401-1.8318	0.2358	151	0.2236	2880	X-RAY DIFFRACTION	95
1.8318-1.9465	0.2304	152	0.2066	2879	X-RAY DIFFRACTION	95
1.9465-2.0968	0.2064	149	0.1839	2836	X-RAY DIFFRACTION	95
2.0968-2.3077	0.1886	152	0.1789	2880	X-RAY DIFFRACTION	94
2.3077-2.6415	0.1669	151	0.1676	2868	X-RAY DIFFRACTION	94
2.6415-3.3273	0.1575	151	0.1363	2866	X-RAY DIFFRACTION	94
3.3273-29.4882	0.1516	149	0.1084	2846	X-RAY DIFFRACTION	92

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	1.3458	0.065	-0.1782	0.2722	0.0037	0.0678	0.0103	-0.0108	-0.0229	0.0905	-0.0404	0.0475	-0.0222	0.0022	0.0285	0.1166	0.0023	-0.0008	0.1171	-0.001	0.1726	43.3671	43.2107	26.6811
2	1.9913	-1.3474	1.4003	3.4881	-3.1769	2.9898	-0.3121	-0.3374	-0.2661	0.118	0.1964	-0.171	0.2328	-0.131	0.0564	0.1766	0.0186	0.0154	0.1507	0.0107	0.1565	48.1156	39.019	34.9613
3	1.4507	0.9033	0.4322	0.7306	0.1042	0.1831	-0.0541	-0.0597	0.079	0.0261	0.0415	-0.0494	0.0147	-0.0177	0.0182	0.1319	0.0069	0.0064	0.1185	-0.0008	0.1659	46.4704	45.0684	26.7809
4	1.2024	-0.0044	-0.2649	1.1081	-0.061	0.123	-0.0269	0.3653	-0.028	-0.1129	0.0059	-0.0676	0.0051	-0.014	0.0195	0.1354	-0.008	0.0141	0.1702	-0.0103	0.1678	41.5288	45.2272	17.8257
5	1.51	1.3327	0.3655	1.9243	0.2822	0.445	0.0171	0.063	-0.28	0.1898	-0.0009	-0.431	-0.0574	0.2041	0.0162	0.1668	-0.0156	-0.0225	0.1533	0.0209	0.2272	60.4443	48.2238	32.1047
6	2.0347	0.1007	0.7298	0.5714	1.064	2.0763	0.5482	-0.5048	0.1249	0.3073	-0.164	0.0027	0.8454	-0.4514	-0.2157	0.3169	-0.1611	-0.0111	0.3959	-0.0199	0.1366	52.7882	51.3813	37.7772
7	2.6887	1.6539	0.4384	2.3702	1.3332	1.5199	0.1188	-0.7497	0.0697	0.2017	-0.761	0.0125	-0.0047	-0.16	0.4594	0.4836	-0.0955	-0.0006	0.7019	0.0272	0.3739	45.3303	42.0747	43.9622
8	0.3523	0.0084	-0.2106	0.2675	0.1992	0.1957	-0.0123	0.1676	-0.0588	-0.1689	-0.0754	-0.0152	-0.0332	0.0549	0.0564	0.228	-0.0076	0.0074	0.2355	-0.0531	0.1427	33.4638	42.4217	66.1119
9	1.5859	0.6967	0.0819	1.7915	-1.0729	0.8447	-0.6305	0.2508	-0.1132	-0.7703	0.3603	-0.0247	-0.5019	0.1975	0.1736	0.3966	-0.0437	-0.0611	0.3511	-0.0806	0.1273	30.1461	37.3303	58.2554
10	1.4111	0.6104	-0.1541	1.2498	-0.2006	-0.0232	-0.2973	0.2135	0.0751	-0.2738	0.1505	0.0945	0.0191	-0.0646	0.0561	0.2115	-0.0167	-0.034	0.2165	-0.0258	0.1496	29.5287	45.6644	64.5043
11	1.0936	0.5369	-0.2355	0.4119	-0.0626	0.202	0.2316	-0.3658	-0.31	0.1223	-0.1077	-0.1645	0.1494	-0.0457	-0.0291	0.2383	-0.0046	-0.0174	0.2384	-0.0102	0.1496	36.9788	39.9338	73.983
12	0.7747	0.1471	-0.4551	0.236	-0.0095	0.2701	0.0192	-0.217	-0.0481	-0.1203	-0.0962	-0.0151	-0.2105	0.0874	0.0708	0.1975	0.0274	0.0156	0.2393	-0.0481	0.1276	26.0484	45.5466	71.2257
13	2.2281	-0.5097	1.3506	2.669	0.6137	1.1581	0.3541	0.3816	0.052	-0.4014	-0.6799	0.357	-0.2214	0.1438	0.3163	0.3748	0.0991	-0.0811	0.4563	-0.0279	0.2185	18.2032	48.5834	57.2751
14	2.9678	-0.5576	-0.4971	1.6303	0.3734	0.1394	0.6346	1.6877	0.1231	-0.5161	-0.1289	0.0888	0.7508	0.2858	-0.3492	0.6193	0.2962	-0.0547	1.1464	-0.1555	0.1828	30.1679	43.5095	50.4558

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 3:27)
2	X-RAY DIFFRACTION	2	(chain A and resid 28:32)
3	X-RAY DIFFRACTION	3	(chain A and resid 33:64)
4	X-RAY DIFFRACTION	4	(chain A and resid 65:76)
5	X-RAY DIFFRACTION	5	(chain A and resid 77:84)
6	X-RAY DIFFRACTION	6	(chain A and resid 85:94)
7	X-RAY DIFFRACTION	7	(chain A and resid 95:101)
8	X-RAY DIFFRACTION	8	(chain B and resid 2:27)
9	X-RAY DIFFRACTION	9	(chain B and resid 28:32)
10	X-RAY DIFFRACTION	10	(chain B and resid 33:54)
11	X-RAY DIFFRACTION	11	(chain B and resid 55:71)
12	X-RAY DIFFRACTION	12	(chain B and resid 72:78)
13	X-RAY DIFFRACTION	13	(chain B and resid 79:90)
14	X-RAY DIFFRACTION	14	(chain B and resid 91:100)

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