PDB-2qw7: Carboxysome Subunit, CcmL

ID or keywords:

Entry

Database: PDB / ID: 2qw7

Title

Carboxysome Subunit, CcmL

Components

Carbon dioxide concentrating mechanism protein ccmL

Keywords

STRUCTURAL PROTEIN / pentamer

Function / homology

EutN/Ccml / Bacterial microcompartment vertex (BMV) domain profile. / Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL / EutN/Ccml superfamily / Ethanolamine utilisation protein EutN/carboxysome / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta / Carboxysome vertex protein CcmL

Function and homology information

Biological species

Synechocystis sp. (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Tanaka, S. / Sawaya, M.R. / Kerfeld, C.A. / Yeates, T.O.

Citation

Journal: Science / Year: 2008
Title: Atomic-level models of the bacterial carboxysome shell.
Authors: Tanaka, S. / Kerfeld, C.A. / Sawaya, M.R. / Cai, F. / Heinhorst, S. / Cannon, G.C. / Yeates, T.O.

History

Deposition	Aug 9, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 4, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Feb 21, 2024	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 / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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	2qw7.cif.gz	190.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2qw7_validation.pdf.gz	537.8 KB	Display	wwPDB validaton report
Full document	2qw7_full_validation.pdf.gz	577.5 KB	Display
Data in XML	2qw7_validation.xml.gz	39.2 KB	Display
Data in CIF	2qw7_validation.cif.gz	54.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qw/2qw7 ftp://data.pdbj.org/pub/pdb/validation_reports/qw/2qw7	HTTPS FTP

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Related structure data

Related structure data	2rcfC 3bn4C 2qyr PDB Unreleased entry 2qzm PDB Unreleased entry C: citing same article (ref.)
Similar structure data	4jvz-d 4yhc-2 6p1y-1 4n8f-d 5u6e-1 5gnm-3 3nvx-1 1uhe-1 5z9j-4 6hqd-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&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 (6)

Deposited unit

A: Carbon dioxide concentrating mechanism protein ccmL

B: Carbon dioxide concentrating mechanism protein ccmL

C: Carbon dioxide concentrating mechanism protein ccmL

D: Carbon dioxide concentrating mechanism protein ccmL

E: Carbon dioxide concentrating mechanism protein ccmL

F: Carbon dioxide concentrating mechanism protein ccmL

G: Carbon dioxide concentrating mechanism protein ccmL

H: Carbon dioxide concentrating mechanism protein ccmL

I: Carbon dioxide concentrating mechanism protein ccmL

J: Carbon dioxide concentrating mechanism protein ccmL

hetero molecules

120 kDa, 10 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Carbon dioxide concentrating mechanism protein ccmL

B: Carbon dioxide concentrating mechanism protein ccmL

C: Carbon dioxide concentrating mechanism protein ccmL

D: Carbon dioxide concentrating mechanism protein ccmL

E: Carbon dioxide concentrating mechanism protein ccmL

hetero molecules

defined by author&software
59.9 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

F: Carbon dioxide concentrating mechanism protein ccmL

G: Carbon dioxide concentrating mechanism protein ccmL

H: Carbon dioxide concentrating mechanism protein ccmL

I: Carbon dioxide concentrating mechanism protein ccmL

J: Carbon dioxide concentrating mechanism protein ccmL

hetero molecules

defined by author&software
59.9 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	64.428, 107.444, 72.264
Angle α, β, γ (deg.)	90.000, 96.510, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
3	1	C
4	1	D
5	1	E
6	1	F
7	1	G
8	1	H
9	1	I
10	1	J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 3 / Auth seq-ID: 1 - 95 / Label seq-ID: 1 - 95

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B
3	C	C
4	D	D
5	E	E
6	F	F
7	G	G
8	H	H
9	I	I
10	J	J

Details

one biological unit corresponds to a pentamer containing chains A,B,C,D,E. another biologinal unit corresponds to a pentamer containing chains F,G,H,I,J.

#1: Protein	Carbon dioxide concentrating mechanism protein ccmL Mass: 11935.568 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ccmL / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: P72759
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.08 Å³/Da / Density % sol: 40.92 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M bis-Tris, 20% PEG3350, 0.3M NaCl, pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 8.2.2 / Wavelength: 0.97944, 0.979617, 0.975593

Detector

Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 14, 2006

Radiation

Monochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97944	1
2	0.979617	1
3	0.975593	1

Reflection

Resolution: 2.4→90 Å / Num. all: 52537 / Num. obs: 52537 / % possible obs: 98 % / Observed criterion σ(F): -3 / Redundancy: 3.3 % / R_merge(I) obs: 0.129 / Χ²: 1.046 / Net I/σ(I): 6.4

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.7 Å / D res low: 19.98 Å / FOM : 0.21 / FOM acentric: 0.212 / FOM centric: 0.14 / Reflection: 26439 / Reflection acentric: 25574 / Reflection centric: 865

Phasing MAD set

Highest resolution: 2.7 Å / Lowest resolution: 19.98 Å

ID	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	0.98	0.95	13.7	17.9	0.35	0.27	25464	857
2	0.98	0.96	14	18.7	0.3	0.21	25518	860
3	2.03	1	0.1	0	0	0	25574	865

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Loc acentric	Loc centric	Power acentric	Power centric	Reflection acentric	Reflection centric
1	11.1-19.98	0.91	0.83	12.6	26.1	0.52	0.32	296	38
1	7.69-11.1	0.93	0.85	13.1	16.3	0.63	0.37	743	63
1	5.88-7.69	0.94	0.9	10.3	18.2	0.64	0.33	1374	84
1	4.76-5.88	0.96	0.92	11.9	15.4	0.53	0.41	2229	102
1	4-4.76	0.98	0.99	13.4	17.7	0.43	0.33	3246	124
1	3.44-4	0.98	0.97	14.5	19.3	0.33	0.22	4511	143
1	3.03-3.44	0.99	1	14.1	16.5	0.31	0.22	5955	167
1	2.7-3.03	0.99	1	14.4	18.8	0.25	0.16	7110	136
2	11.1-19.98	0.97	1.05	10.6	17.4	0.47	0.36	296	38
2	7.69-11.1	0.95	0.94	10.8	16.2	0.6	0.29	743	63
2	5.88-7.69	0.95	0.91	10.4	21.5	0.51	0.22	1374	84
2	4.76-5.88	0.97	0.92	12.2	17.6	0.42	0.29	2229	101
2	4-4.76	0.98	0.98	13.3	19.9	0.36	0.24	3248	124
2	3.44-4	0.99	0.96	14.6	18.7	0.29	0.19	4512	144
2	3.03-3.44	0.99	0.99	14.8	19.7	0.26	0.16	5955	169
2	2.7-3.03	0.99	1	15	17.3	0.22	0.15	7161	137
3	11.1-19.98	1.38	1	0.1	0.1	0	0	296	38
3	7.69-11.1	1.44	1	0.1	0	0	0	743	63
3	5.88-7.69	1.91	1	0.1	0	0	0	1374	84
3	4.76-5.88	1.46	1	0.1	0	0	0	2229	102
3	4-4.76	1.48	1	0.1	0	0	0	3249	124
3	3.44-4	1.68	1	0	0	0	0	4515	144
3	3.03-3.44	2.69	1	0.1	0	0	0	5959	170
3	2.7-3.03	3.54	1	0	0	0	0	7209	140

Phasing MAD set site

ID	Atom type symbol	B iso	Fract x	Fract y	Fract z	Occupancy
1	Se	39.26	1	0.402	0.024	0.065
2	Se	26.098	1.041	0.413	-0.102	0.05
3	Se	12.586	1.154	0.485	-0.125	0.059
4	Se	33.843	1.13	0.57	-0.177	0.039
5	Se	40.104	1.125	0.649	-0.08	0.058
6	Se	18.692	1.004	0.696	-0.043	0.046
7	Se	20.516	0.946	0.67	0.088	0.05
8	Se	27.89	0.831	0.612	0.123	0.045
9	Se	22.275	0.863	0.516	0.156	0.056
10	Se	16.178	0.858	0.436	0.085	0.046
11	Se	27.569	0.503	0.245	0.473	0.053
12	Se	33.195	0.46	0.256	0.601	0.05
13	Se	22.906	0.342	0.329	0.624	0.055
14	Se	31.718	0.365	0.413	0.678	0.047
15	Se	30.869	0.375	0.492	0.58	0.051
16	Se	3.726	0.493	0.538	0.542	0.041
17	Se	31.847	0.551	0.513	0.411	0.057
18	Se	46.065	0.668	0.456	0.378	0.044
19	Se	35.209	0.633	0.359	0.343	0.058
20	Se	22.256	0.64	0.28	0.416	0.047
21	Se	30.533	0.999	0.403	0.025	0.042
22	Se	19.238	1.041	0.413	-0.101	0.038
23	Se	15.497	1.155	0.485	-0.124	0.044
24	Se	31.608	1.132	0.569	-0.177	0.038
25	Se	21.278	1.126	0.65	-0.082	0.034
26	Se	12.545	1.005	0.695	-0.042	0.035
27	Se	14.485	0.947	0.671	0.089	0.042
28	Se	16.5	0.83	0.613	0.122	0.032
29	Se	14.92	0.865	0.517	0.157	0.043
30	Se	12.7	0.858	0.436	0.085	0.032
31	Se	24.204	0.502	0.246	0.473	0.042
32	Se	27.461	0.459	0.256	0.6	0.038
33	Se	24.742	0.345	0.329	0.624	0.048
34	Se	20.489	0.366	0.413	0.678	0.04
35	Se	14.285	0.374	0.493	0.581	0.036
36	Se	11.815	0.496	0.538	0.544	0.041
37	Se	15.531	0.551	0.513	0.412	0.042
38	Se	31.654	0.668	0.456	0.379	0.031
39	Se	19.558	0.634	0.36	0.342	0.044
40	Se	22.835	0.641	0.28	0.415	0.036
41	Se	20.867	0.997	0.4	0.023	0
42	Se	5.058	1.04	0.409	-0.103	0
43	Se	10.85	1.156	0.482	-0.126	0
44	Se	30.049	1.136	0.566	-0.174	0
45	Se	21.79	1.125	0.648	-0.078	0
46	Se	19.759	1.003	0.691	-0.045	0
47	Se	7.555	0.948	0.67	0.087	0
48	Se	34.778	0.83	0.609	0.123	0
49	Se	14.483	0.856	0.515	0.154	0
50	Se	2.486	0.859	0.433	0.085	0
51	Se	19.622	0.503	0.242	0.475	0
52	Se	20.316	0.461	0.251	0.604	0
53	Se	8.813	0.342	0.326	0.626	0
54	Se	24.154	0.363	0.409	0.676	0
55	Se	20.318	0.372	0.491	0.58	0
56	Se	18.324	0.497	0.533	0.547	0
57	Se	3.087	0.551	0.512	0.413	0
58	Se	31.15	0.675	0.455	0.382	0
59	Se	19.598	0.641	0.358	0.346	0
60	Se	7.777	0.64	0.276	0.416	0

Phasing MAD shell

Resolution (Å)	FOM	FOM acentric	FOM centric	Reflection	Reflection acentric	Reflection centric
11.1-19.98	0.298	0.302	0.271	334	296	38
7.69-11.1	0.336	0.348	0.196	806	743	63
5.88-7.69	0.331	0.338	0.225	1458	1374	84
4.76-5.88	0.277	0.281	0.196	2331	2229	102
4-4.76	0.237	0.241	0.126	3373	3249	124
3.44-4	0.214	0.217	0.129	4659	4515	144
3.03-3.44	0.195	0.199	0.08	6129	5959	170
2.7-3.03	0.143	0.144	0.083	7349	7209	140

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Processing

Software

Name	Version	Classification	NB
REFMAC		refinement
PDB_EXTRACT	3	data extraction

Refinement

Method to determine structure:

MAD / Resolution: 2.4→19.9 Å / Cor.coef. F_o:F_c: 0.944 / Cor.coef. F_o:F_c free: 0.917 / SU B: 25.057 / SU ML: 0.288 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.398 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.296	1511	5 %	RANDOM
R_work	0.24	-	-	-
obs	0.243	30053	78.92 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 22.143 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.03 Å²	0 Å²	-0.02 Å²
2-	-	0.03 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→19.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7155	0	24	90	7269

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	7328
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	4962
X-RAY DIFFRACTION	r_angle_refined_deg	2.404	1.993	9898
X-RAY DIFFRACTION	r_angle_other_deg	2.353	3	12173
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.014	5	960
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.342	24.191	272
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.684	15	1309
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.569	15	59
X-RAY DIFFRACTION	r_chiral_restr	0.136	0.2	1198
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	8038
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	1339
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.3	1334
X-RAY DIFFRACTION	r_nbd_other	0.243	0.3	5271
X-RAY DIFFRACTION	r_nbtor_refined	0.18	0.5	3276
X-RAY DIFFRACTION	r_nbtor_other	0.107	0.5	4465
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.262	0.5	450
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.119	0.5	8
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.287	0.3	22
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.283	0.3	88
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.286	0.5	5
X-RAY DIFFRACTION	r_mcbond_it	2.713	2	5986
X-RAY DIFFRACTION	r_mcbond_other	0.244	2	1999
X-RAY DIFFRACTION	r_mcangle_it	3.532	3	7595
X-RAY DIFFRACTION	r_scbond_it	3.756	2	2935
X-RAY DIFFRACTION	r_scangle_it	4.945	3	2296

Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	A	549	TIGHT POSITIONAL	0.08	0.05
2	B	549	TIGHT POSITIONAL	0.07	0.05
3	C	549	TIGHT POSITIONAL	0.06	0.05
4	D	549	TIGHT POSITIONAL	0.06	0.05
5	E	549	TIGHT POSITIONAL	0.07	0.05
6	F	549	TIGHT POSITIONAL	0.06	0.05
7	G	549	TIGHT POSITIONAL	0.06	0.05
8	H	549	TIGHT POSITIONAL	0.08	0.05
9	I	549	TIGHT POSITIONAL	0.06	0.05
10	J	549	TIGHT POSITIONAL	0.06	0.05
1	A	597	LOOSE POSITIONAL	0.75	5
2	B	597	LOOSE POSITIONAL	0.79	5
3	C	597	LOOSE POSITIONAL	0.84	5
4	D	597	LOOSE POSITIONAL	0.82	5
5	E	597	LOOSE POSITIONAL	0.88	5
6	F	597	LOOSE POSITIONAL	1.04	5
7	G	597	LOOSE POSITIONAL	0.82	5
8	H	597	LOOSE POSITIONAL	1.02	5
9	I	597	LOOSE POSITIONAL	0.9	5
10	J	597	LOOSE POSITIONAL	0.76	5
1	A	549	TIGHT THERMAL	0.27	0.5
2	B	549	TIGHT THERMAL	0.25	0.5
3	C	549	TIGHT THERMAL	0.17	0.5
4	D	549	TIGHT THERMAL	0.2	0.5
5	E	549	TIGHT THERMAL	0.22	0.5
6	F	549	TIGHT THERMAL	0.18	0.5
7	G	549	TIGHT THERMAL	0.18	0.5
8	H	549	TIGHT THERMAL	0.22	0.5
9	I	549	TIGHT THERMAL	0.19	0.5
10	J	549	TIGHT THERMAL	0.46	0.5
1	A	597	LOOSE THERMAL	3.79	10
2	B	597	LOOSE THERMAL	3.55	10
3	C	597	LOOSE THERMAL	3.35	10
4	D	597	LOOSE THERMAL	3.38	10
5	E	597	LOOSE THERMAL	3.68	10
6	F	597	LOOSE THERMAL	3.52	10
7	G	597	LOOSE THERMAL	3.54	10
8	H	597	LOOSE THERMAL	3.37	10
9	I	597	LOOSE THERMAL	3.37	10
10	J	597	LOOSE THERMAL	3.3	10

LS refinement shell

Resolution: 2.4→2.464 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.719	29	-
R_work	0.297	554	-
all	-	583	-
obs	-	-	21.15 %

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	1.3084	-0.0054	-0.4565	3.2253	0.0676	1.2991	0.158	-0.0235	0.174	-0.1529	0.0624	-0.1852	-0.0456	-0.039	-0.2204	-0.1847	0.0166	-0.1427	-0.0287	0.0025	-0.2441	68.065	58.0088	3.7642
2	1.275	-0.0756	-0.4379	2.5899	0.2639	1.2607	-0.1214	0.0067	-0.1536	-0.0965	0.0587	-0.1372	0.1014	-0.0556	0.0627	-0.0934	0.0117	-0.0141	-0.0581	0.012	-0.1266	32.0339	95.0465	39.7481

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 96	1 - 96
2	X-RAY DIFFRACTION	1	B	B	1 - 96	1 - 96
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