PDB-3ssq: CcmK2 - form 1 dodecamer

ID or keywords:

Entry

Database: PDB / ID: 3ssq

Title

CcmK2 - form 1 dodecamer

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: 2.2 Å

Authors

Samborska, B. / Kimber, M.S.

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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Download

PDBx/mmCIF format	3ssq.cif.gz	246 KB	Display	PDBx/mmCIF format
PDB format	pdb3ssq.ent.gz	202.1 KB	Display	PDB format
PDBx/mmJSON format	3ssq.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	3ssrC 3sssC 2a1bS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3ssr-1 2xqt-1 6lad-d 5suh-1 5djb-5 2xqu-1 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

A: Carbon dioxide concentrating mechanism protein

B: Carbon dioxide concentrating mechanism protein

C: Carbon dioxide concentrating mechanism protein

D: Carbon dioxide concentrating mechanism protein

E: Carbon dioxide concentrating mechanism protein

F: Carbon dioxide concentrating mechanism protein

hetero molecules

78.8 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Carbon dioxide concentrating mechanism protein

B: Carbon dioxide concentrating mechanism protein

C: Carbon dioxide concentrating mechanism protein

D: Carbon dioxide concentrating mechanism protein

E: Carbon dioxide concentrating mechanism protein

F: Carbon dioxide concentrating mechanism protein

hetero molecules

A: Carbon dioxide concentrating mechanism protein

B: Carbon dioxide concentrating mechanism protein

C: Carbon dioxide concentrating mechanism protein

D: Carbon dioxide concentrating mechanism protein

E: Carbon dioxide concentrating mechanism protein

F: Carbon dioxide concentrating mechanism protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	83.362, 83.362, 226.860
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Carbon dioxide concentrating mechanism protein Mass: 13090.877 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermosynechococcus elongatus (bacteria) Strain: BP-1 / Gene: ccmK2, tll0947 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q8DKB2
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 231 / 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: 2.51 Å³/Da / Density % sol: 50.97 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 30 % PEG 2000 MME, 0.21 M (NH4)2SO4, 0.1 M Na acetate , pH 4.6, 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: 0.97934 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 23, 2008 Details: White beam slits, cryo-cooled first and sagittally bent second crystal of double crystal monochromator (DCM), vertically focusing mirror (VFM)
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97934 Å / Relative weight: 1
Reflection	Resolution: 2.2→40 Å / Num. all: 41410 / Num. obs: 41410 / % possible obs: 99.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / R_sym value: 0.05 / Net I/σ(I): 14.2
Reflection shell	Resolution: 2.2→2.28 Å / Mean I/σ(I) obs: 2.5 / Num. unique all: 4005 / R_sym value: 0.525 / % possible all: 98.4

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Processing

Software

Name	Version	Classification
MxDC		data collection
MOLREP		phasing
REFMAC	5.2.0019	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 2A1B

2a1b

Resolution: 2.2→40 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.956 / SU B: 15.915 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2366	2064	5 %	RANDOM
R_work	0.18663	-	-	-
all	0.18907	41410	-	-
obs	0.18907	39066	98.83 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 59.565 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.75 Å²	0 Å²	0 Å²
2-	-	1.75 Å²	0 Å²
3-	-	-	-3.5 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4510	0	10	231	4751

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	4581
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3072
X-RAY DIFFRACTION	r_angle_refined_deg	1.401	1.961	6213
X-RAY DIFFRACTION	r_angle_other_deg	0.974	3	7462
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.082	5	596
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.895	22.581	186
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.015	15	756
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.633	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	746
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	5140
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	924
X-RAY DIFFRACTION	r_nbd_refined	0.181	0.2	810
X-RAY DIFFRACTION	r_nbd_other	0.195	0.2	3257
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	2200
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	2523
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	153
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.32	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.232	0.2	36
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.2	5
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.654	1.5	3862
X-RAY DIFFRACTION	r_mcbond_other	0.11	1.5	1240
X-RAY DIFFRACTION	r_mcangle_it	0.776	2	4812
X-RAY DIFFRACTION	r_scbond_it	1.423	3	1758
X-RAY DIFFRACTION	r_scangle_it	2.036	4.5	1401
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.477	140	-
R_work	0.442	2686	-
obs	-	-	93.7 %

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	7.4712	-3.4333	-0.4591	5.719	-2.1064	1.4188	0.01	0.0247	0.5063	-0.0052	0.0195	-0.2955	-0.6388	-0.1189	-0.0295	-0.016	-0.1823	0.1607	-0.3196	-0.0298	-0.2352	25.3195	13.2088	52.1076
2	6.0933	-1.0362	0.666	2.4658	-1.3165	0.7052	0.0132	-0.1473	0.1375	0.0198	0.0437	-0.2473	-0.4503	0.0105	-0.0569	-0.0078	-0.1566	0.184	-0.2185	-0.0291	-0.2179	24.4964	11.5947	54.4534
3	5.9084	-1.673	0.5338	1.1869	-0.1981	4.5885	0.0065	-0.3465	0.9247	0.2711	-0.0441	-0.1522	-0.7858	-0.0861	0.0376	0.1077	-0.1357	0.1746	-0.2836	-0.0635	-0.0819	23.4732	19.6798	55.9457
4	17.4039	-5.7683	-6.6266	3.8039	5.5406	8.4343	-0.0234	0.0672	1.2769	0.018	0.4389	-0.4726	-0.2112	0.3142	-0.4154	0.131	-0.1565	0.2564	-0.3752	0.0938	-0.122	27.0345	17.7606	48.3879
5	9.4294	-1.8178	5.8737	1.237	-2.103	5.0817	-0.0771	-1.787	0.0143	0.0318	0.4739	-0.1198	-0.4395	-0.8205	-0.3968	0.1769	-0.0547	0.2204	0.0475	0.0316	-0.1183	13.3672	12.254	61.352
6	2.0073	-0.8691	-1.7452	5.0613	1.4958	4.3526	0.0441	0.0509	0.1315	-0.1921	0.2222	-0.7414	-0.4046	0.3643	-0.2663	-0.2344	-0.1914	0.1844	-0.2469	-0.1027	-0.1816	37.1944	-3.3834	49.1943
7	4.629	-0.8249	-0.5901	4.5466	-1.1437	0.5493	0.1027	-0.1626	-0.0999	-0.0681	0.0424	-0.4581	-0.2344	0.2393	-0.1451	-0.2224	-0.1223	0.1802	-0.2226	-0.1252	-0.211	36.1099	-4.601	52.0769
8	4.0481	-1.2674	-2.2129	3.9138	-1.0192	2.0431	0.0258	-0.7516	0.2161	0.1455	0.1846	-0.8973	-0.8515	0.5283	-0.2104	-0.2006	-0.2596	0.1527	-0.1427	-0.1675	-0.0451	42.1216	-0.1966	55.6119
9	3.808	0.5883	-0.8327	7.52	4.2372	6.9949	-0.3525	-0.1386	0.1644	-0.8016	0.4561	-1.0148	-0.9949	0.7644	-0.1036	-0.2379	-0.2438	0.2977	-0.258	-0.0236	-0.0868	41.2692	0.7435	47.1882
10	1.2967	-1.0323	-0.04	6.5904	-1.619	0.8279	-0.3839	-0.6421	-0.0133	0.9742	0.3428	-0.4458	-0.2161	0.3572	0.0411	0.0282	-0.1104	0.1195	-0.07	-0.0254	-0.2301	31.21	-1.232	63.8253
11	4.6847	1.9082	1.7565	3.916	0.7945	3.849	-0.0377	0.2304	-0.1828	-0.5905	0.3344	-0.4233	-0.086	0.4276	-0.2968	-0.0659	-0.1233	0.2258	-0.2487	-0.1153	-0.2104	30.7751	-18.1194	37.9007
12	3.8892	1.4211	0.4654	1.5558	2.3612	4.6872	-0.1831	0.1006	-0.2755	-0.2854	0.4172	-0.1608	-0.0128	0.2114	-0.2341	-0.0273	-0.1164	0.161	-0.2934	-0.064	-0.2704	29.762	-19.8164	40.4975
13	4.0313	0.9932	-1.3849	3.209	2.473	3.1473	-0.0261	0.0942	-0.5328	-0.3185	0.5086	-0.969	0.0848	0.6265	-0.4826	-0.0833	-0.0674	0.164	-0.1785	-0.2056	-0.0232	37.4684	-22.6987	41.1586
14	1.8594	-0.0412	1.0539	2.4655	1.1798	8.3856	0.039	0.5384	-0.1441	-0.5318	0.3252	-0.4666	-0.2321	1.1179	-0.3642	0.0016	-0.1582	0.328	-0.1977	-0.1498	-0.0363	35.9004	-17.3834	34.8219
15	3.5572	5.9866	2.5674	12.9248	2.4812	3.0405	0.4035	-0.4186	-0.3494	0.6343	-0.0936	-0.6896	0.7592	0.0096	-0.3099	-0.0316	-0.0542	0.0997	-0.1561	-0.0132	-0.1592	31.7709	-21.2899	53.5539
16	3.6554	-1.9904	0.3738	6.4642	0.287	3.406	0.0659	0.1	0.1214	-0.5687	0.0331	0.0053	0.0351	-0.1931	-0.099	0.1829	-0.1252	0.1155	-0.2569	-0.0349	-0.2663	13.1681	-17.0892	29.2302
17	3.0751	-2.6704	-0.5755	2.7533	-0.3883	1.9232	0.0042	-0.168	-0.1248	-0.3574	0.1915	0.0781	0.1715	-0.3801	-0.1957	0.152	-0.133	0.0471	-0.206	0.0394	-0.2636	11.7356	-18.8611	31.667
18	2.6887	-2.426	-1.3219	7.407	-1.4143	2.3636	0.143	0.1865	-0.2515	-0.7245	0.0476	0.0651	0.4242	-0.125	-0.1906	0.2195	-0.1213	0.0452	-0.2182	-0.0369	-0.1946	14.1301	-25.5649	27.321
19	5.1255	-5.7048	1.6218	12.4347	-1.4244	0.8967	0.3304	0.5403	-0.0933	-1.0462	-0.1963	-0.0175	-0.0494	-0.0094	-0.1341	0.2842	-0.0975	0.2268	-0.1537	-0.0146	-0.2573	16.3173	-17.9658	23.985
20	9.576	0.9748	4.0573	3.0895	0.3342	1.7211	0.142	-0.7917	-0.8289	-0.1313	0.2426	0.1939	0.405	-0.5207	-0.3846	0.1893	-0.1338	0.1206	-0.0631	0.1049	-0.1457	14.5181	-27.9716	40.8085
21	3.3753	0.027	-0.3532	8.2257	1.9673	2.6734	-0.0675	0.165	0.2152	-0.4607	0.1339	0.521	-0.0313	-0.4039	-0.0664	0.1541	-0.0382	-0.0142	-0.1934	0.109	-0.2545	1.1484	-1.9574	31.5121
22	2.287	-1.8911	0.1329	4.4009	0.3771	2.9677	0.1006	-0.0276	0.1935	-0.4531	0.1761	0.4259	-0.0591	-0.5908	-0.2767	0.0903	-0.0278	0.0698	-0.1998	0.1251	-0.1742	0.1192	-2.6421	34.074
23	2.7012	-2.6439	0.7431	3.5994	1.2009	3.8799	-0.0862	0.3816	-0.3084	-0.7614	0.0583	0.8338	-0.0424	-0.7552	0.0279	0.2088	-0.0582	-0.0624	-0.006	0.1381	-0.0572	-4.5733	-5.8679	28.0708
24	3.9121	1.3974	-0.0932	12.8775	1.869	0.721	-0.1034	0.4543	0.2508	-1.2633	0.1525	0.5613	-0.1707	-0.28	-0.0491	0.3084	-0.0473	-0.0029	-0.0823	0.1274	-0.2839	1.9873	-0.9018	25.606
25	8.997	-7.6607	-3.7097	8.61	3.2777	1.5364	-0.4759	-0.1819	-0.6127	0.2039	0.4475	1.3632	0.211	-0.4417	0.0284	0.1447	-0.105	0.1149	0.0248	0.1736	-0.0484	-3.5061	-14.6519	38.5301
26	3.9689	0.3814	-0.2269	4.06	0.4986	5.2669	0.0474	-0.2245	0.0431	-0.1325	0.0936	0.2623	-0.5139	-0.0571	-0.141	0.0413	-0.0148	0.1448	-0.3772	0.0779	-0.2094	8.2441	13.6251	42.7905
27	2.6416	-0.538	-1.2584	4.8036	1.2229	5.0546	0.2398	-0.0516	0.239	0.3963	-0.2927	0.1472	-0.3315	-0.4626	0.053	0.0427	-0.0866	0.1198	-0.3258	0.0548	-0.2168	6.5458	12.5368	45.3982
28	1.5718	0.5862	1.264	4.8914	1.4587	4.8636	-0.1175	-0.3866	0.269	-0.2668	-0.0183	0.8414	-0.7074	-0.6821	0.1357	0.1335	0.0779	0.094	-0.2537	0.0626	-0.0907	0.0639	16.6984	42.3738
29	6.585	2.5724	-1.3292	5.8536	-1.6451	4.5605	0.393	0.617	0.5742	-0.3298	-0.1447	0.3022	-0.3871	-0.109	-0.2484	0.2285	0.0709	0.1847	-0.4604	0.1022	-0.2509	7.2806	16.9805	37.5914
30	0.9717	1.7785	1.0225	6.7981	6.8828	8.1641	0.239	-0.4411	0.5529	0.4976	-0.5508	0.8672	-0.0208	-0.7984	0.3118	0.1073	-0.0433	0.1975	-0.0141	0.1195	0.0019	-4.0226	5.3519	48.7732

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 21
2	X-RAY DIFFRACTION	2	A	22 - 41
3	X-RAY DIFFRACTION	3	A	42 - 61
4	X-RAY DIFFRACTION	4	A	62 - 81
5	X-RAY DIFFRACTION	5	A	82 - 101
6	X-RAY DIFFRACTION	6	B	2 - 21
7	X-RAY DIFFRACTION	7	B	22 - 41
8	X-RAY DIFFRACTION	8	B	42 - 61
9	X-RAY DIFFRACTION	9	B	62 - 81
10	X-RAY DIFFRACTION	10	B	82 - 101
11	X-RAY DIFFRACTION	11	C	2 - 21
12	X-RAY DIFFRACTION	12	C	22 - 41
13	X-RAY DIFFRACTION	13	C	42 - 61
14	X-RAY DIFFRACTION	14	C	62 - 81
15	X-RAY DIFFRACTION	15	C	82 - 101
16	X-RAY DIFFRACTION	16	D	2 - 21
17	X-RAY DIFFRACTION	17	D	22 - 41
18	X-RAY DIFFRACTION	18	D	42 - 61
19	X-RAY DIFFRACTION	19	D	62 - 81
20	X-RAY DIFFRACTION	20	D	82 - 101
21	X-RAY DIFFRACTION	21	E	1 - 21
22	X-RAY DIFFRACTION	22	E	22 - 41
23	X-RAY DIFFRACTION	23	E	42 - 61
24	X-RAY DIFFRACTION	24	E	62 - 81
25	X-RAY DIFFRACTION	25	E	82 - 101
26	X-RAY DIFFRACTION	26	F	2 - 21
27	X-RAY DIFFRACTION	27	F	22 - 41
28	X-RAY DIFFRACTION	28	F	42 - 61
29	X-RAY DIFFRACTION	29	F	62 - 81
30	X-RAY DIFFRACTION	30	F	82 - 101

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