PDB-7mpv: CmcC from Type II Cut MCP

ID or keywords:

Entry

Database: PDB / ID: 7mpv

Title

CmcC from Type II Cut MCP

Components

BMC domain-containing protein

Keywords

STRUCTURAL PROTEIN / microcompartment / MCP / shell protein / Cut MCP / choline utilization

Function / homology

Function and homology information

ethanolamine catabolic process / bacterial microcompartment
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.292 Å

Authors

Ochoa, J.M. / Mijares, O. / Sawaya, M.R. / Yeates, T.O.

Funding support

United States, 1items

Citation

Journal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments
Authors: Ochoa, J.M. / Mijares, O. / Acosta, A.A. / Escoto, X. / Leon-Rivera, N. / Marshall, J.D. / Sawaya, M.R. / Yeates, T.O.

History

Deposition	May 5, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 8, 2021	Provider: repository / Type: Initial release
Revision 1.1	Apr 3, 2024	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mpv.cif.gz	374.9 KB	Display	PDBx/mmCIF format
PDB format	pdb7mpv.ent.gz	310.8 KB	Display	PDB format
PDBx/mmJSON format	7mpv.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mpv_validation.pdf.gz	511.7 KB	Display	wwPDB validaton report
Full document	7mpv_full_validation.pdf.gz	520 KB	Display
Data in XML	7mpv_validation.xml.gz	33.4 KB	Display
Data in CIF	7mpv_validation.cif.gz	49.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mp/7mpv ftp://data.pdbj.org/pub/pdb/validation_reports/mp/7mpv	HTTPS FTP

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Related structure data

Related structure data	7mgpC 7mmxC 7mn4C 7mpwC 7mpxC C: citing same article (ref.)
Similar structure data	4rbt-1 7mpv-2 4p7t-d 4qig-1 7mmx-2 4qie-1 7mpw-d 4p7v-d 4p2s-2 4p2s-1 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 - 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: BMC domain-containing protein

B: BMC domain-containing protein

C: BMC domain-containing protein

D: BMC domain-containing protein

E: BMC domain-containing protein

F: BMC domain-containing protein

G: BMC domain-containing protein

H: BMC domain-containing protein

I: BMC domain-containing protein

J: BMC domain-containing protein

K: BMC domain-containing protein

L: BMC domain-containing protein

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

1

A: BMC domain-containing protein

B: BMC domain-containing protein

C: BMC domain-containing protein

D: BMC domain-containing protein

E: BMC domain-containing protein

F: BMC domain-containing protein

defined by author&software
Evidence: gel filtration, CmcC elutes as a hexamer. The elution profile is consistent with a predicted approximate molecular mass of 62 KDa.
62.5 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: BMC domain-containing protein

H: BMC domain-containing protein

I: BMC domain-containing protein

J: BMC domain-containing protein

K: BMC domain-containing protein

L: BMC domain-containing protein

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

Unit cell

Length a, b, c (Å)	50.600, 56.290, 92.030
Angle α, β, γ (deg.)	96.310, 90.080, 98.550
Int Tables number	1
Space group name H-M	P1

#1: Protein	BMC domain-containing protein / Propanediol utilization protein PduA / Putative propanediol utilization protein: polyhedral bodies ...Propanediol utilization protein PduA / Putative propanediol utilization protein: polyhedral bodies pduJ or pduA Mass: 10415.908 Da / Num. of mol.: 12 / Mutation: K25A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pduA_3, pduA / Plasmid: pET-22b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V7
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

BMC domain-containing protein / Propanediol utilization protein PduA / Putative propanediol utilization protein: polyhedral bodies ...

Mass: 10415.908 Da / Num. of mol.: 12 / Mutation: K25A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli (E. coli) / Gene: pduA_3, pduA / Plasmid: pET-22b(+) / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8G9V7

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.06 Å³/Da / Density % sol: 40.32 %
Crystal grow	Temperature: 294 K / Method: vapor diffusion, hanging drop Details: 0.1 M HEPES pH 7.5, 10% PEG 8000, 8% Ethylene glycol

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 24-ID-C / Wavelength: 0.9786 Å

Detector

Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 18, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9786 Å / Relative weight: 1

Reflection

Resolution: 2.29→91.46 Å / Num. obs: 41777 / % possible obs: 93.2 % / Redundancy: 3.65 % / B_iso Wilson estimate: 47.53 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.077 / R_rim(I) all: 0.09 / Χ²: 0.909 / Net I/σ(I): 8.69 / Num. measured all: 152490 / Scaling rejects: 35

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.29-2.35	3.414	0.632	1.71	9542	3330	2795	0.875	0.744	83.9
2.35-2.42	3.74	0.514	2.23	11574	3232	3095	0.924	0.599	95.8
2.42-2.49	3.704	0.441	2.56	11154	3133	3011	0.932	0.515	96.1
2.49-2.56	3.715	0.373	2.92	10996	3098	2960	0.957	0.435	95.5
2.56-2.65	3.711	0.303	3.52	10258	2911	2764	0.968	0.354	95
2.65-2.74	3.625	0.243	4.06	9613	2826	2652	0.979	0.285	93.8
2.74-2.84	3.487	0.208	4.68	8993	2801	2579	0.981	0.245	92.1
2.84-2.96	3.776	0.17	5.95	9746	2676	2581	0.988	0.197	96.4
2.96-3.09	3.784	0.153	6.61	9187	2526	2428	0.991	0.178	96.1
3.09-3.24	3.694	0.116	8.24	8562	2424	2318	0.993	0.136	95.6
3.24-3.42	3.657	0.089	10.48	7983	2343	2183	0.994	0.105	93.2
3.42-3.62	3.536	0.071	12.95	7036	2197	1990	0.995	0.084	90.6
3.62-3.87	3.589	0.071	13.91	6791	2045	1892	0.995	0.083	92.5
3.87-4.18	3.68	0.054	17.09	6657	1915	1809	0.997	0.064	94.5
4.18-4.58	3.667	0.05	20.33	6095	1768	1662	0.997	0.058	94
4.58-5.13	3.617	0.048	20.55	5306	1599	1467	0.997	0.057	91.7
5.13-5.92	3.546	0.049	19.37	4326	1384	1220	0.997	0.058	88.2
5.92-7.25	3.679	0.045	21.73	4121	1201	1120	0.997	0.053	93.3
7.25-10.25	3.625	0.031	27.44	2951	915	814	0.999	0.037	89
10.25-91.46	3.659	0.036	27.02	1599	494	437	0.998	0.042	88.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.3 Å	55.32 Å
Translation	2.3 Å	55.32 Å

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Processing

Software

Name	Version	Classification
BUSTER		refinement
XSCALE		data scaling
PHASER	2.8.3	phasing
PDB_EXTRACT	3.27	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: D_1000255588

Resolution: 2.292→91.46 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.9 / SU R Cruickshank DPI: 0.424 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.391 / SU R_free Blow DPI: 0.255 / SU R_free Cruickshank DPI: 0.264

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2685	4178	10 %	RANDOM
R_work	0.2329	-	-	-
obs	0.2364	41777	93.2 %	-

Displacement parameters

B_iso max: 118.22 Å² / B_iso mean: 70.11 Å² / B_iso min: 33.53 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.7849 Å²	10.5378 Å²	-23.6267 Å²
2-	-	8.0863 Å²	14.0666 Å²
3-	-	-	-5.3014 Å²

Refine analyze

Luzzati coordinate error obs: 0.41 Å

Refinement step

Cycle: final / Resolution: 2.292→91.46 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7267	0	0	132	7399
B_iso mean	-	-	-	58.33	-
Num. residues	-	-	-	-	1031

Refine LS restraints

Refine-ID	Type	Number	Restraint function	Weight	Dev ideal
X-RAY DIFFRACTION	t_dihedral_angle_d	2530	SINUSOIDAL	2
X-RAY DIFFRACTION	t_trig_c_planes
X-RAY DIFFRACTION	t_gen_planes	1289	HARMONIC	5
X-RAY DIFFRACTION	t_it	7304	HARMONIC	10
X-RAY DIFFRACTION	t_nbd
X-RAY DIFFRACTION	t_improper_torsion
X-RAY DIFFRACTION	t_pseud_angle
X-RAY DIFFRACTION	t_chiral_improper_torsion	1036	SEMIHARMONIC	5
X-RAY DIFFRACTION	t_sum_occupancies
X-RAY DIFFRACTION	t_utility_distance
X-RAY DIFFRACTION	t_utility_angle
X-RAY DIFFRACTION	t_utility_torsion
X-RAY DIFFRACTION	t_ideal_dist_contact	5732	SEMIHARMONIC	4
X-RAY DIFFRACTION	t_bond_d	7304	HARMONIC	2	0.005
X-RAY DIFFRACTION	t_angle_deg	9894	HARMONIC	2	0.83
X-RAY DIFFRACTION	t_omega_torsion				2.29
X-RAY DIFFRACTION	t_other_torsion				15.6

LS refinement shell

Resolution: 2.292→2.31 Å / R_factor R_free error: 0

	R_factor	Num. reflection	% reflection
R_free	0.5138	83	9.93 %
R_work	0.4148	753	-
obs	-	-	65.14 %

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	3.6566	1.5654	-2.7023	5.5719	2.6452	5.5417	-0.2658	0.1877	-0.1303	-0.1809	0.276	-0.3728	0.0575	-0.065	-0.0102	-0.1418	-0.0654	0.1574	-0.1124	-0.1467	0.0162	-6.9516	5.7762	-9.6526
2	5.5836	2.0426	-2.8158	4.6967	0.5788	2.1843	-0.4571	0.4619	-0.344	0.1109	0.1409	-0.1376	0.3001	-0.1982	0.3162	-0.0713	-0.1448	0.2147	-0.1696	-0.1752	0.0245	-23.9167	-6.5181	-2.91
3	3.6693	-0.3489	-4.1414	4.6558	2.0302	5.8993	0.053	-0.0339	-0.0188	-0.128	0.2256	-0.4355	-0.2188	0.1259	-0.2786	-0.1516	-0.1384	0.1441	-0.0948	-0.1367	0.0085	-2.5955	25.6581	-0.066
4	4.2536	0.1241	-2.9874	3.4294	1.7126	3.0608	0.1428	-0.1127	0.0884	-0.0272	0.1899	-0.3298	-0.2478	0.0165	-0.3327	-0.0281	-0.0697	0.0902	-0.1437	-0.095	-0.0157	-16.0249	32.6753	13.9517
5	6.2302	0.3754	-2.2293	3.8205	2.434	5.4854	-0.1984	0.2118	-0.0642	0.1449	-0.105	0.1393	0.2672	-0.313	0.3034	-0.066	-0.0599	0.1361	-0.2061	-0.0551	-0.0076	-36.8931	1.9982	12.1865
6	2.3443	2.1161	-1.2804	9.6583	-0.3138	1.0211	-0.1471	0.3418	-0.1943	0.5124	-0.3671	0.7027	0.2512	-0.2986	0.5141	-0.08	0.0784	-0.1053	-0.0054	0.0917	-0.1069	-32.6578	22.9866	20.7469
7	3.7314	2.9712	1.1512	4.8813	3.2834	3.2439	-0.2224	-0.0536	-0.063	-0.5258	0.3689	-0.2374	-0.3988	0.3321	-0.1465	0.0188	-0.1196	0.2374	-0.1829	-0.1188	-0.0489	-10.4593	0.1892	31.5257
8	1.4922	2.0455	-1.4268	4.3994	2.0225	4.8949	0.1867	0.0548	0.231	0.3624	-0.3729	0.1276	0.5245	-0.2335	0.1862	0.0614	-0.1051	0.1898	-0.1696	-0.0911	-0.0443	-24.0058	-11.2714	40.2582
9	7.1024	0.6666	-6.1498	5.2106	1.2422	11.7276	0.4136	-0.4994	0.356	-0.1379	0.2384	-0.1686	-0.43	0.674	-0.6519	-0.1003	-0.2872	0.2641	-0.1762	-0.2506	-0.0544	-2.4264	19.7733	43.1871
10	6.8901	0.7734	-5.3517	4.4204	2.8642	7.0652	0.4285	-0.6951	0.6163	-0.1008	0.2163	-0.2653	-0.5347	0.5504	-0.6447	0.0664	-0.2935	0.3154	-0.1405	-0.274	-0.0339	-13.0344	24.7713	61.3654
11	5.226	-0.337	-3.637	5.0588	2.63	7.784	-0.0134	0.0506	0.0577	0.5001	-0.4117	0.1426	0.6586	-0.3497	0.4251	0.0534	-0.288	0.3048	-0.1622	-0.1907	-0.1178	-34.3314	-5.8193	58.6271
12	4.0778	2.5373	-2.9441	8.1065	3.7163	6.7162	0.3708	-0.2646	0.1566	0.2013	-0.6103	0.5371	0.0029	-0.1349	0.2395	-0.04	-0.1945	0.286	-0.1241	-0.212	-0.1111	-28.8099	12.7817	68.8963

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	{ A\|* }	A	3 - 87
2	X-RAY DIFFRACTION	2	{ B\|* }	B	0 - 87
3	X-RAY DIFFRACTION	3	{ C\|* }	C	2 - 81
4	X-RAY DIFFRACTION	4	{ D\|* }	D	2 - 89
5	X-RAY DIFFRACTION	5	{ E\|* }	E	0 - 88
6	X-RAY DIFFRACTION	6	{ F\|* }	F	-4 - 86
7	X-RAY DIFFRACTION	7	{ G\|* }	G	-5 - 86
8	X-RAY DIFFRACTION	8	{ H\|* }	H	3 - 86
9	X-RAY DIFFRACTION	9	{ I\|* }	I	2 - 82
10	X-RAY DIFFRACTION	10	{ J\|* }	J	3 - 86
11	X-RAY DIFFRACTION	11	{ K\|* }	K	2 - 85
12	X-RAY DIFFRACTION	12	{ L\|* }	L	2 - 86

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