PDB-4liw: CcmK1 Carboxysome Shell Protein from Synechocystis PCC6803, L11K ...

ID or keywords:

Entry

Database: PDB / ID: 4liw

Title

CcmK1 Carboxysome Shell Protein from Synechocystis PCC6803, L11K Point Mutant

Components

Carbon dioxide-concentrating mechanism protein CcmK homolog 1

Keywords

TRANSPORT PROTEIN / bacterial microcompartment / carboxysome / BMC shell protein / twinning / translational NCS

Function / homology

Function and homology information

structural constituent of carboxysome shell / carboxysome / carbon fixation / photosynthesis
Similarity search - Function

Biological species

Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.6 Å

Authors

Thompson, M.C. / Yeates, T.O.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A challenging interpretation of a hexagonally layered protein structure.
Authors: Thompson, M.C. / Yeates, T.O.

History

Deposition	Jul 3, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 8, 2014	Provider: repository / Type: Initial release
Revision 1.1	Feb 12, 2014	Group: Database references
Revision 1.2	Apr 4, 2018	Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen Item: _diffrn_source.type / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 1.3	Sep 20, 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

-
Download

PDBx/mmCIF format	4liw.cif.gz	83 KB	Display	PDBx/mmCIF format
PDB format	pdb4liw.ent.gz	63.9 KB	Display	PDB format
PDBx/mmJSON format	4liw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4liw_validation.pdf.gz	447.8 KB	Display	wwPDB validaton report
Full document	4liw_full_validation.pdf.gz	449.1 KB	Display
Data in XML	4liw_validation.xml.gz	9.2 KB	Display
Data in CIF	4liw_validation.cif.gz	12 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/li/4liw ftp://data.pdbj.org/pub/pdb/validation_reports/li/4liw	HTTPS FTP

-
Related structure data

Related structure data	3dncS S: Starting model for refinement
Similar structure data	3dn9-d 3bn4-d 3cim-2 5fgr-d 3dnc-1 5l38-1 4qig-2 3cim-1 4qig-1 3nwg-2 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#114 - Jun 2009 Vaults similarity (8) #165 - Sep 2013 Designed Protein Cages similarity (4)

Deposited unit

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

hetero molecules

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

1

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

hetero molecules

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

hetero molecules

A: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

B: Carbon dioxide-concentrating mechanism protein CcmK homolog 1

hetero molecules

defined by author&software
64.7 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	70.020, 70.020, 56.250
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	173
Space group name H-M	P6₃

Details

THE BIOLOGICAL UNIT IS A HEXAMER, WHICH CAN BE GENERATED BY APPLYING THE FOLLOWING SYMMETRY OPERATIONS TO THE TWO CHAINS (A AND B) IN THE ASYMMETRIC UNIT. CHAIN A: (X, Y, Z), (-X+Y, -X+1, Z), AND (-Y+1, X-Y+1, Z). CHAIN B: (X, Y, Z), (-Y-1, X-Y+1, Z), AND (-X+Y, -X+1, Z).

#1: Protein	Carbon dioxide-concentrating mechanism protein CcmK homolog 1 Mass: 10740.304 Da / Num. of mol.: 2 / Mutation: L11K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 substr. Kazusa (bacteria) Strain: PCC6803 / Gene: ccmK1, sll1029 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P72760
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 1.85 Å³/Da / Density % sol: 33.62 %
Crystal grow	Temperature: 298 K / pH: 9.5 Details: 0.1M N-cyclohexyl-2-aminoethanesulfonic acid, 1.26M ammonium sulfate, 0.15M sodium chloride, 0.01M guanidinium chloride, pH 9.5, vapor diffusion, hanging drop, temperature 298K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418
Detector	Type: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Nov 22, 2011
Radiation	Monochromator: CONFOCAL MIRRORS VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection twin	Operator: K,H,-L / Fraction: 0.6
Reflection	Resolution: 1.6→41.24 Å / Num. obs: 20387 / % possible obs: 98 % / Observed criterion σ(I): -3 / B_iso Wilson estimate: 25.05 Å² / R_merge(I) obs: 0.055 / Net I/σ(I): 34.07
Reflection shell	Resolution: 1.6→1.64 Å / R_merge(I) obs: 0.244 / Mean I/σ(I) obs: 5.55 / % possible all: 84.6

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.5.4	phasing
PHENIX	dev_1334	refinement
PDB_EXTRACT	3.11	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DNC

3dnc

Resolution: 1.6→41.24 Å / Occupancy max: 1 / Occupancy min: 0.16 / σ(F): 1.37 / Phase error: 34.4 / Stereochemistry target values: TWIN_LSQ_F
Details: REFINEMENT WAS CARRIED OUT WITH HYDROGEN ATOMS IN THE RIDING POSITIONS FOR THE PURPOSES OF MAINTAINING GOOD GEOMETRY AND INCLUDING THEIR SCATTERING CONTRIBUTIONS IN CALCULATED STRUCTURE ...

	R_factor	Num. reflection	% reflection
R_free	0.195	1034	5.07 %
R_work	0.18	-	-
obs	0.192	20387	98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 21.53 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→41.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1359	0	5	51	1415

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	1408
X-RAY DIFFRACTION	f_angle_d	1.315	1916
X-RAY DIFFRACTION	f_dihedral_angle_d	16.749	516
X-RAY DIFFRACTION	f_chiral_restr	0.068	235
X-RAY DIFFRACTION	f_plane_restr	0.004	247

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 (%)
1.6013-1.6857	0.2825	134	0.2804	2493	X-RAY DIFFRACTION	85
1.6857-1.7913	0.2853	149	0.28	2788	X-RAY DIFFRACTION	94
1.7913-1.9296	0.2605	144	0.2497	2758	X-RAY DIFFRACTION	94
1.9296-2.1238	0.1816	151	0.2128	2803	X-RAY DIFFRACTION	94
2.1238-2.4311	0.2234	150	0.2011	2804	X-RAY DIFFRACTION	95
2.4311-3.0627	0.1898	154	0.1777	2805	X-RAY DIFFRACTION	95
3.0627-41.2529	0.1801	151	0.1505	2873	X-RAY DIFFRACTION	95

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	2.6832	-1.0445	-0.4626	2.1735	0.2359	1.3208	-0.0687	0.0087	0.0502	0.0934	-0.0322	0.1005	0.009	0.0143	0.0829	0.1233	0.0005	-0.0041	0.1136	0.0033	0.0476	-1.6509	60.0537	6.2345
2	0.3712	0.0298	-0.072	1.4729	0.7973	0.5817	0.0406	-0.1117	0.0844	0.0488	-0.1582	0.0811	-0.0405	-0.0301	0.0915	0.1137	-0.0254	0.0016	0.1276	0.0097	0.1087	8.4844	62.986	7.916
3	2.1316	0.7334	0.238	0.9881	-1.0454	1.7196	0.0153	-0.4489	0.0861	0.2528	-0.1435	-0.0233	-0.0368	-0.018	0.0479	0.1298	0.0117	0.03	0.1529	-0.0073	0.1847	1.3175	59.0468	13.1891
4	1.7157	-0.3169	-0.3104	2.5399	-0.2564	1.1079	-0.0637	0.0248	-0.0392	0.1052	-0.1	-0.0509	0.0946	-0.0723	0.196	0.0729	-0.0058	0.0006	0.1256	-0.004	0.0871	-0.4836	56.7686	8.0639
5	3.6991	-1.722	-2.1324	2.5716	1.0563	2.5727	0.0159	-0.1376	0.3003	-0.0129	0.1132	0.0651	-0.3453	0.0227	-0.0955	0.1728	0.0099	-0.0044	0.127	-0.0199	0.2191	-0.4925	71.6463	6.5772
6	2.0048	2.892	-2.6239	2.8783	1.4174	2.6302	0.1524	0.2829	0.3168	-0.2016	0.0081	0.1634	-0.3262	0.0232	-0.0161	0.2281	-0.0004	0.0101	0.1345	0.0313	0.1033	6.9974	65.1776	-0.7478
7	2.5306	0.8475	-0.8949	5.7469	-0.2862	2.303	-0.0797	0.0205	0.3445	-0.1093	-0.0918	-0.1297	-0.0562	-0.0397	0.1038	0.1627	0.0173	0.0153	0.177	0.0321	0.1533	12.3361	60.5357	-2.7232
8	1.734	0.1391	0.3071	0.7325	-0.6217	0.6587	-0.0468	0.2506	0.1327	-0.1485	-0.02	0.1161	-0.0188	0.0662	0.0514	0.1182	0.0018	-0.014	0.1135	0.008	0.0615	-3.5428	61.3142	1.8974
9	8.0257	3.6095	-2.5555	7.5099	-0.616	0.9692	-0.1386	-0.338	-0.1907	0.5026	-0.128	-0.051	-0.2109	0.1357	0.159	0.1961	0.1107	0.0916	0.0994	-0.0633	0.2914	-14.8503	66.3045	14.4491
10	3.3835	-0.8455	0.6753	2.1144	-0.0578	0.98	-0.0116	-0.3528	-0.0576	-0.0258	-0.126	-0.2109	-0.0001	-0.0244	0.1925	0.2514	0.0012	0.0456	0.2316	0.0209	0.0951	-9.0435	58.0911	17.8335
11	1.9336	1.1758	0.7368	2.8939	1.2529	1.5163	-0.0074	-0.1518	0.3532	0.0495	-0.0531	-0.057	0.0329	0.0217	0.0069	0.0948	-0.0103	-0.0016	0.1293	-0.0141	0.1161	17.4007	54.4479	7.7962
12	1.4403	0.5379	-0.0224	1.9978	0.3437	1.2074	0.0236	-0.2006	0.0662	-0.0985	0.0123	-0.212	0.0445	0.117	-0.0467	0.0968	0.0268	0.0167	0.1415	0.0126	0.0934	20.4277	42.7783	5.982
13	4.6227	-1.3833	-2.3249	1.2648	-0.2514	2.2314	0.0603	-0.2234	0.3109	0.2363	-0.0042	-0.3595	-0.1418	0.131	-0.0417	0.1089	0.0099	-0.0331	0.207	-0.073	0.1659	26.9146	51.3865	13.2618
14	2.0191	0.6087	-0.0018	1.8342	0.1876	0.936	-0.0294	-0.2665	0.0115	0.0543	-0.0913	0.016	0.0638	-0.0322	0.0304	0.097	0.0089	-0.0002	0.1148	0.0015	0.0741	12.3686	47.787	8.9645
15	0.9787	0.1717	-0.2998	3.1912	1.9753	1.5679	-0.0273	-0.1005	0.312	-0.0108	0.0339	-0.2383	-0.0882	0.0715	-0.0356	0.0132	-0.0024	0.0408	0.1764	-0.001	0.4465	26.8209	57.6342	7.1057
16	2.8727	-1.3267	1.9572	5.0065	2.3624	3.7607	0.0725	0.1409	0.2161	-0.2185	0.0684	-0.2744	-0.1834	0.3099	-0.0536	0.1665	0.0045	0.0619	0.2318	0.009	0.133	25.4905	47.2169	-0.046
17	4.4725	-1.0297	-0.1121	4.5008	0.0723	3.613	-0.0797	0.1591	0.0779	-0.1312	0.0355	-0.2854	-0.1543	0.1288	0.0336	0.1751	0.0056	0.0342	0.1978	-0.0073	0.0792	22.1228	40.2906	-2.7527
18	2.1739	0.287	0.2133	3.5761	0.9472	1.0678	0.04	0.1141	0.5583	0.0038	0.0106	-0.2863	-0.0048	0.201	-0.1249	0.1096	-0.0029	0.0062	0.0547	0.012	0.1819	15.9624	59.8286	7.187
19	3.5347	-1.7266	-2.7526	0.8645	1.557	3.9464	-0.0546	-0.25	-0.3091	0.1496	0.083	0.0531	0.3306	-0.0209	0.0223	0.429	0.0236	0.2319	0.234	-0.0039	-0.7189	9.7197	61.5154	18.4095
20	1.3972	0.26	-1.0853	3.0503	0.2463	0.9082	0.0064	-0.2077	-0.1088	0.189	0.0631	-0.326	0.0852	0.1416	0.0108	0.7284	0.3085	0.4086	0.1113	-0.1686	-0.0642	10.955	55.7808	16.3933

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain A and resid 2:12)
2	X-RAY DIFFRACTION	2	(chain A and resid 13:27)
3	X-RAY DIFFRACTION	3	(chain A and resid 28:37)
4	X-RAY DIFFRACTION	4	(chain A and resid 38:48)
5	X-RAY DIFFRACTION	5	(chain A and resid 49:60)
6	X-RAY DIFFRACTION	6	(chain A and resid 61:64)
7	X-RAY DIFFRACTION	7	(chain A and resid 65:70)
8	X-RAY DIFFRACTION	8	(chain A and resid 71:79)
9	X-RAY DIFFRACTION	9	(chain A and resid 80:83)
10	X-RAY DIFFRACTION	10	(chain A and resid 84:94)
11	X-RAY DIFFRACTION	11	(chain B and resid 3:10)
12	X-RAY DIFFRACTION	12	(chain B and resid 11:23)
13	X-RAY DIFFRACTION	13	(chain B and resid 24:32)
14	X-RAY DIFFRACTION	14	(chain B and resid 33:47)
15	X-RAY DIFFRACTION	15	(chain B and resid 48:58)
16	X-RAY DIFFRACTION	16	(chain B and resid 59:64)
17	X-RAY DIFFRACTION	17	(chain B and resid 65:71)
18	X-RAY DIFFRACTION	18	(chain B and resid 72:83)
19	X-RAY DIFFRACTION	19	(chain B and resid 84:87)
20	X-RAY DIFFRACTION	20	(chain B and resid 88:92)

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi