PDB-3pxg: Structure of MecA121 and ClpC1-485 complex

ID or keywords:

Entry

Database: PDB / ID: 3pxg

Title

Structure of MecA121 and ClpC1-485 complex

Components

Adapter protein mecA 1
Negative regulator of genetic competence ClpC/MecB

Keywords

PROTEIN BINDING / ClpB / proteolysis / ClpC / ClpX / Hsp100/Clp / AAA+ proteins

Function / homology

Function and homology information

negative regulation of establishment of competence for transformation / negative regulation of sporulation resulting in formation of a cellular spore / establishment of competence for transformation / sporulation resulting in formation of a cellular spore / protein-macromolecule adaptor activity / ATP hydrolysis activity / ATP binding
Similarity search - Function

Biological species

Bacillus subtilis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3.654 Å

Authors

Wang, F. / Mei, Z.Q. / Wang, J.W. / Shi, Y.G.

Citation

Journal: Nature / Year: 2011
Title: Structure and mechanism of the hexameric MecA-ClpC molecular machine.
Authors: Wang, F. / Mei, Z. / Qi, Y. / Yan, C. / Hu, Q. / Wang, J. / Shi, Y.

History

Deposition	Dec 9, 2010	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 16, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Apr 11, 2012	Group: Refinement description
Revision 1.3	Oct 16, 2013	Group: Database references
Revision 1.4	Nov 1, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3pxg.cif.gz	1.3 MB	Display	PDBx/mmCIF format
PDB format	pdb3pxg.ent.gz	1.1 MB	Display	PDB format
PDBx/mmJSON format	3pxg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3pxg_validation.pdf.gz	509.6 KB	Display	wwPDB validaton report
Full document	3pxg_full_validation.pdf.gz	564.9 KB	Display
Data in XML	3pxg_validation.xml.gz	101.2 KB	Display
Data in CIF	3pxg_validation.cif.gz	139.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/px/3pxg ftp://data.pdbj.org/pub/pdb/validation_reports/px/3pxg	HTTPS FTP

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Related structure data

Related structure data	2y1qC 2y1rSC 3pxiC 1qvrS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	0208 2750 0204 0191 3998 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	#80 - Aug 2006 AAA+ Proteases similarity (4) #176 - Aug 2014 Dynein similarity (4) #150 - Jun 2012 Sliding Clamps similarity (1)

Deposited unit

a: Adapter protein mecA 1

A: Negative regulator of genetic competence ClpC/MecB

b: Adapter protein mecA 1

B: Negative regulator of genetic competence ClpC/MecB

c: Adapter protein mecA 1

C: Negative regulator of genetic competence ClpC/MecB

d: Adapter protein mecA 1

D: Negative regulator of genetic competence ClpC/MecB

e: Adapter protein mecA 1

E: Negative regulator of genetic competence ClpC/MecB

f: Adapter protein mecA 1

F: Negative regulator of genetic competence ClpC/MecB

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	137.56, 137.56, 445.65
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:
NCS ensembles :

ID
1
2
3

#1: Protein	Adapter protein mecA 1 Mass: 11533.901 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 121-218 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET-27a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37958
#2: Protein	Negative regulator of genetic competence ClpC/MecB Mass: 52076.953 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-485 / Mutation: E280A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET-27a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37571

#1: Protein

Adapter protein mecA 1

Mass: 11533.901 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 121-218
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Plasmid: pET-27a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37958

#2: Protein

Negative regulator of genetic competence ClpC/MecB

Mass: 52076.953 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 1-485 / Mutation: E280A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Bacillus subtilis (bacteria) / Plasmid: pET-27a / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P37571

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.19 Å³/Da / Density % sol: 61.43 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 12% PEG 3350, 450mM sodium malonate, 100mM MES, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2009
Radiation	Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 3.654→49.524 Å / Num. obs: 53303 / % possible obs: 96.1 % / Observed criterion σ(I): 19.34 / Redundancy: 5.2 % / B_iso Wilson estimate: 115.2 Å² / R_merge(I) obs: 0.081 / Net I/σ(I): 19.34
Reflection shell	Resolution: 3.65→3.78 Å / Redundancy: 4.3 % / R_merge(I) obs: 0.732 / Mean I/σ(I) obs: 1.64 / Num. unique all: 4185 / % possible all: 76.5

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Processing

Software

Name	Version	Classification
BSS		data collection
PHASER		phasing
PHENIX	(phenix.refine: 1.6_289)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2Y1R, 1QVR

2y1r

1qvr

Resolution: 3.654→49.524 Å / SU ML: 0.79 / σ(F): 1.34 / Stereochemistry target values: ML
Details: LINKING BETWEEN RESIDUE (C ALA 280) AND RESIDUE (C ILE 299) WAS DUE TO THE POOR DENSITY

	R_factor	Num. reflection	% reflection
R_free	0.303	2858	5.37 %
R_work	0.2574	-	-
obs	0.26	53221	96.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 287.8 Å² / k_sol: 0.32 e/Å³

Displacement parameters

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.861 Å²	0 Å²	0 Å²
2-	-	-2.861 Å²	-0 Å²
3-	-	-	5.3788 Å²

Refinement step

Cycle: LAST / Resolution: 3.654→49.524 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24809	0	0	0	24809

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.114	26784
X-RAY DIFFRACTION	f_angle_d	1.985	35480
X-RAY DIFFRACTION	f_dihedral_angle_d	24.447	15824
X-RAY DIFFRACTION	f_chiral_restr	0.093	3939
X-RAY DIFFRACTION	f_plane_restr	0.005	4408

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type	Rms dev position (Å)
1	1	A	1085	X-RAY DIFFRACTION	POSITIONAL
1	2	B	1085	X-RAY DIFFRACTION	POSITIONAL	0.058
1	3	C	1085	X-RAY DIFFRACTION	POSITIONAL	0.061
1	4	D	1070	X-RAY DIFFRACTION	POSITIONAL	0.059
1	5	E	1070	X-RAY DIFFRACTION	POSITIONAL	0.052
1	6	F	1085	X-RAY DIFFRACTION	POSITIONAL	0.055
2	1	A	2263	X-RAY DIFFRACTION	POSITIONAL
2	2	C	2263	X-RAY DIFFRACTION	POSITIONAL	0.064
2	3	D	2272	X-RAY DIFFRACTION	POSITIONAL	0.053
2	4	E	2272	X-RAY DIFFRACTION	POSITIONAL	0.062
2	5	F	2272	X-RAY DIFFRACTION	POSITIONAL	0.067
3	1	A	772	X-RAY DIFFRACTION	POSITIONAL
3	2	B	772	X-RAY DIFFRACTION	POSITIONAL	0.069
3	3	C	772	X-RAY DIFFRACTION	POSITIONAL	0.069
3	4	D	772	X-RAY DIFFRACTION	POSITIONAL	0.058
3	5	E	772	X-RAY DIFFRACTION	POSITIONAL	0.056
3	6	F	772	X-RAY DIFFRACTION	POSITIONAL	0.053

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	% reflection obs (%)
3.6543-3.7172	0	0	0.4015	2100	75
3.7172-3.7848	0.4455	867	0.3764	1306	81
3.7848-3.8576	0	0	0.3674	2340	86
3.8576-3.9363	0	0	0.3466	2500	91
3.9363-4.0219	0	0	0.3266	2557	95
4.0219-4.1154	0	0	0.3084	2637	97
4.1154-4.2182	0	0	0.2891	2710	99
4.2182-4.3322	0	0	0.2798	2751	100
4.3322-4.4596	0.3289	628	0.2557	2098	100
4.4596-4.6035	0.3216	254	0.2239	2503	100
4.6035-4.7679	0	0	0.2069	2747	100
4.7679-4.9586	0	0	0.218	2737	100
4.9586-5.184	0	0	0.2408	2748	100
5.184-5.457	0	0	0.2396	2742	100
5.457-5.7984	0.3211	682	0.2471	2089	100
5.7984-6.2454	0	0	0.2414	2796	100
6.2454-6.8724	0	0	0.2368	2794	100
6.8724-7.8634	0	0	0.2208	2782	100
7.8634-9.8941	0.2255	356	0.1897	2525	100
9.8941-49.5285	0.2187	71	0.206	2901	99

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	6.7407	0.4535	1.0726	2.6157	2.5085	3.3765	-0.7693	-0.9636	-2.4122	0.7426	1.2262	-0.4316	1.0911	0.9477	-0.3104	1.0044	0.4499	0.2818	0.8716	-0.4419	2.0426	16.3414	-111.5454	95.1634
2	4.4905	-2.3267	-0.5833	6.4972	2.9915	3.1096	-0.0122	-0.2996	0.4401	1.2419	-0.6931	1.021	0.4798	-0.0365	-0.1987	0.9164	-0.4412	-0.1943	0.6316	-0.298	0.4415	-25.2355	-77.7649	83.59
3	8.6999	5.3754	5.4976	5.7733	3.1604	3.2494	-0.027	-1.2571	1.4468	0.3216	-0.0061	0.8044	-0.1937	-1.1154	0.1491	0.2344	0.1542	0.0121	1.1079	0.2456	0.0742	-18.7643	-23.9882	86.2141
4	8.5083	-2.8708	4.8918	2.0493	-0.9518	3.2367	-1.5516	-0.805	1.8747	1.0847	0.89	-1.0913	-0.6262	-0.7556	-0.4079	0.6533	-0.2618	0.6146	0.4187	0.6328	-0.132	30.7081	-4.5147	99.1725
5	3.9756	-1.2316	1.91	2.8584	1.2483	2.3447	1.0237	1.3813	0.3571	1.3176	0.0527	-2.1631	1.0582	0.2478	-0.7601	1.102	0.1862	0.4266	1.1861	0.1834	1.9812	72.7806	-37.6312	111.9471
6	8.2285	3.4809	5.3903	4.1277	0.6765	4.0881	0.2672	-1.3674	-2.0318	-0.4377	-0.1483	-1.1888	-0.6133	-0.9604	-0.0203	0.7655	0.4137	0.645	1.7455	-0.236	3.1291	65.2749	-92.134	110.9313
7	7.1798	-5.5241	2.5392	1.7165	-1.0551	0.5074	0.9482	-0.6509	-1.8453	-0.671	0.2374	0.6837	0.5298	-0.0867	-0.3449	0.4526	-0.044	0.1788	0.5655	-0.0726	1.1445	-2.5819	-92.0527	123.1675
8	1.5655	0.3821	0.9178	7.2803	1.3061	1.5768	-0.7994	-0.5026	0.7697	0.2039	0.5518	1.7659	0.2039	0.1727	0.1934	0.3531	0.1407	0.1832	0.5716	-0.0459	0.6201	-22.9402	-59.0856	115.5394
9	4.606	4.1061	1.991	2.5194	1.8311	2.0063	0.0805	1.1284	0.6931	0.4528	-0.2379	-0.007	0.1016	0.2761	-0.1407	0.838	0.3431	0.0315	0.9295	-0.0027	0.8567	-5.3299	-24.729	123.8161
10	6.2393	-2.0451	2.9746	0.5174	-1.2097	2.2528	0.2274	-0.9981	0.7395	0.1738	-0.5313	-0.3705	-0.2928	-0.3166	0.3234	0.7381	-0.0157	-0.2147	0.8935	-0.147	1.4362	32.7716	-22.5472	133.9253
11	1.1754	-0.2627	-0.3499	5.8116	0.0472	0.6307	-0.1636	-0.2742	-0.0042	0.298	0.2331	-0.4321	-0.0088	-0.133	-0.1344	0.1524	-0.0265	-0.1997	0.4824	0.1501	0.5283	53.8868	-56.2636	139.4082
12	4.6236	-1.8637	1.1552	1.5518	0.3913	1.3496	1.0136	0.0042	-0.1209	0.041	-0.3791	0.5341	0.0601	-0.0996	-0.5524	0.6295	-0.3161	0.0298	0.5708	0.2023	0.8668	35.967	-91.3454	134.5446
13	3.2418	3.6479	0.1244	3.632	0.5084	1.7859	-0.3308	0.522	-2.2149	-0.3377	1.0184	-0.3015	0.4681	1.3829	-0.6549	1.2221	0.3287	-0.2593	2.306	-0.8551	3.963	40.7476	-113.6021	103.2615
14	3.121	-0.719	-3.8365	3.1659	-0.7074	6.1075	-0.158	0.0496	-2.1235	-0.0232	-0.6226	-1.6094	0.9599	0.2758	0.6617	0.5912	-0.2024	-0.1342	0.4191	-0.103	1.3247	-12.7345	-99.5309	85.0636
15	4.1829	-2.0438	-1.6679	5.5811	-1.8761	2.7849	-0.1751	0.2157	-1.9906	-0.4324	0.4719	0.4908	1.3618	-1.0146	0.1571	0.2404	-0.0484	-0.0973	0.3924	-0.1765	1.0517	-32.3823	-45.2773	82.8163
16	8.1588	-1.3857	-4.6353	3.9801	-0.898	9.304	-0.4917	1.5098	1.3655	0.2625	-0.1708	1.2	-0.8792	-1.2822	0.6439	0.6782	-0.2071	-0.3452	0.5654	0.1592	1.0896	6.7695	-3.4012	92.0166
17	6.3741	0.171	-3.0371	0.6993	-0.3908	4.4007	0.3571	0.765	0.2978	-0.7632	-0.9766	-1.4803	-0.3311	0.7019	0.6089	0.7158	0.1055	0.2407	1.2444	0.6487	1.5116	61.1592	-15.7529	107.6286
18	0.3126	0.7296	-0.9062	2.4644	0.6926	8.6803	-0.3392	-0.4106	-0.9066	0.3172	-0.026	-1.4583	-1.116	1.115	0.2483	1.4433	0.2865	0.4166	1.4039	0.3154	4.0787	78.5312	-70.7656	113.833

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN A AND RESID 1:149
2	X-RAY DIFFRACTION	2	CHAIN B AND RESID 1:149
3	X-RAY DIFFRACTION	3	CHAIN C AND RESID 1:149
4	X-RAY DIFFRACTION	4	CHAIN D AND RESID 1:149
5	X-RAY DIFFRACTION	5	CHAIN E AND RESID 1:149
6	X-RAY DIFFRACTION	6	CHAIN F AND RESID 1:149
7	X-RAY DIFFRACTION	7	CHAIN A AND RESID 150:485
8	X-RAY DIFFRACTION	8	CHAIN B AND RESID 150:485
9	X-RAY DIFFRACTION	9	CHAIN C AND RESID 150:485
10	X-RAY DIFFRACTION	10	CHAIN D AND RESID 150:485
11	X-RAY DIFFRACTION	11	CHAIN E AND RESID 150:485
12	X-RAY DIFFRACTION	12	CHAIN F AND RESID 150:485
13	X-RAY DIFFRACTION	13	CHAIN a
14	X-RAY DIFFRACTION	14	CHAIN b
15	X-RAY DIFFRACTION	15	CHAIN c
16	X-RAY DIFFRACTION	16	CHAIN d
17	X-RAY DIFFRACTION	17	CHAIN e
18	X-RAY DIFFRACTION	18	CHAIN f

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