PDB-2c8t: The 3.0 A Resolution Structure of Caseinolytic Clp Protease 1 fro...

ID or keywords:

Entry

Database: PDB / ID: 2c8t

Title

The 3.0 A Resolution Structure of Caseinolytic Clp Protease 1 from Mycobacterium tuberculosis

Components

ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

Keywords

HYDROLASE / SERINE PROTEASE / CLPP1

Function / homology

Function and homology information

endopeptidase Clp / endopeptidase Clp complex / ATP-dependent peptidase activity / protein quality control for misfolded or incompletely synthesized proteins / ATPase binding / serine-type endopeptidase activity / plasma membrane / cytoplasm / cytosol
Similarity search - Function

Biological species

MYCOBACTERIUM TUBERCULOSIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 3 Å

Authors

Ingvarsson, H. / Hogbom, M. / Jones, T.A. / Unge, T.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2007
Title: Insights Into the Inter-Ring Plasticity of Caseinolytic Proteases from the X-Ray Structure of Mycobacterium Tuberculosis Clpp1.
Authors: Ingvarsson, H. / Mate, M.J. / Hogbom, M. / Portnoi, D. / Benaroudj, N. / Alzari, P.M. / Ortiz-Lombardia, M. / Unge, T.

History

Deposition	Dec 7, 2005	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 6, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Refinement description / Version format compliance
Revision 1.2	Dec 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2c8t.cif.gz	437.3 KB	Display	PDBx/mmCIF format
PDB format	pdb2c8t.ent.gz	362.1 KB	Display	PDB format
PDBx/mmJSON format	2c8t.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2c8t_validation.pdf.gz	547.6 KB	Display	wwPDB validaton report
Full document	2c8t_full_validation.pdf.gz	596.9 KB	Display
Data in XML	2c8t_validation.xml.gz	79.9 KB	Display
Data in CIF	2c8t_validation.cif.gz	105.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c8/2c8t ftp://data.pdbj.org/pub/pdb/validation_reports/c8/2c8t	HTTPS FTP

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Related structure data

Related structure data	2cbyC 2ce3C 1tyfS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2ce3-d 4u0h-1 21196 6vgn-d 3hln-2 6vgk-d 3hln-1 7950 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

Deposited unit

A: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

B: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

C: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

D: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

E: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

F: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

G: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

H: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

I: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

J: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

K: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

L: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

M: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

N: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

314 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by software

2

A: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

B: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

C: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

D: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

E: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

F: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

G: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

defined by author&software
157 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

H: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

I: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

J: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

K: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

L: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

M: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

N: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1

defined by author&software
157 kDa, 7 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.719, 168.218, 103.761
Angle α, β, γ (deg.)	90.00, 114.60, 90.00
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
11	1	K
12	1	L
13	1	M
14	1	N

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	14 - 193
2	1	1	1	B	14 - 193
3	1	1	1	C	14 - 193
4	1	1	1	D	14 - 193
5	1	1	1	E	14 - 193
6	1	1	1	F	14 - 193
7	1	1	1	G	14 - 193
8	1	1	1	H	14 - 193
9	1	1	1	I	14 - 193
10	1	1	1	J	14 - 193
11	1	1	1	K	14 - 193
12	1	1	1	L	14 - 193
13	1	1	1	M	14 - 193
14	1	1	1	N	14 - 193

#1: Protein	ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 / CASEINOLYTIC CLP PROTEASE 1 / ENDOPEPTIDASE CLP Mass: 22408.385 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET101D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A526, UniProt: P9WPC5*PLUS, endopeptidase Clp

#1: Protein

ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1 / CASEINOLYTIC CLP PROTEASE 1 / ENDOPEPTIDASE CLP

Mass: 22408.385 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET101D-TOPO / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P0A526, UniProt: P9WPC5*PLUS, endopeptidase Clp

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.97 Å³/Da / Density % sol: 58.21 %
Crystal grow	pH: 5.2 Details: 5 MG/ML PROTEIN, 100 MM TRI-NA-CITRATE, PH 5.2, 3% PEG 4000

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Data collection

Diffraction	Mean temperature: 110 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
Detector	Type: MARRESEARCH / Detector: CCD / Date: Mar 7, 2005
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.931 Å / Relative weight: 1
Reflection	Resolution: 3→59.4 Å / Num. obs: 60193 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / R_merge(I) obs: 0.1 / Net I/σ(I): 5.9
Reflection shell	Resolution: 3→3.16 Å / R_merge(I) obs: 0.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0005	refinement
MOSFLM		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TYF

1tyf

Resolution: 3→19.87 Å / Cor.coef. F_o:F_c: 0.917 / Cor.coef. F_o:F_c free: 0.894 / SU B: 39.873 / SU ML: 0.323 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R Free: 0.414 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.238	3036	5 %	RANDOM
R_work	0.213	-	-	-
obs	0.214	57087	100 %	-

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: 14.94 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.34 Å²	0 Å²	-0.1 Å²
2-	-	-0.31 Å²	0 Å²
3-	-	-	-0.12 Å²

Refinement step

Cycle: LAST / Resolution: 3→19.87 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	18482	0	0	0	18482

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	18816
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.447	1.965	25410
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.316	5	2366
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.586	23.667	840
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.549	15	3248
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	27.437	15	140
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	2898
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	14070
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.233	0.2	9021
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.32	0.2	12906
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.124	0.2	604
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	0.395	0.2	45
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.341	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	0.379	1.5	12121
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.576	2	18914
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.971	3	7392
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.692	4.5	6496
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Ens-ID: 1 / Number: 1322 / Refine-ID: X-RAY DIFFRACTION

Dom-ID	Auth asym-ID	Type	Rms dev position (Å)	Weight position
1	A	tight positional	0.04	0.05
2	B	tight positional	0.04	0.05
3	C	tight positional	0.05	0.05
4	D	tight positional	0.05	0.05
5	E	tight positional	0.05	0.05
6	F	tight positional	0.06	0.05
7	G	tight positional	0.06	0.05
8	H	tight positional	0.05	0.05
9	I	tight positional	0.06	0.05
10	J	tight positional	0.05	0.05
11	K	tight positional	0.04	0.05
12	L	tight positional	0.06	0.05
13	M	tight positional	0.05	0.05
14	N	tight positional	0.04	0.05
1	A	tight thermal	0.07	0.5
2	B	tight thermal	0.07	0.5
3	C	tight thermal	0.09	0.5
4	D	tight thermal	0.1	0.5
5	E	tight thermal	0.08	0.5
6	F	tight thermal	0.1	0.5
7	G	tight thermal	0.09	0.5
8	H	tight thermal	0.09	0.5
9	I	tight thermal	0.11	0.5
10	J	tight thermal	0.08	0.5
11	K	tight thermal	0.07	0.5
12	L	tight thermal	0.1	0.5
13	M	tight thermal	0.08	0.5
14	N	tight thermal	0.08	0.5

LS refinement shell

Resolution: 3→3.08 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.323	214
R_work	0.3	4095

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	2.3585	0.0498	-2.0592	7.4282	0.3669	5.6038	-0.042	-0.0459	0.009	-0.9157	0.1087	-0.3457	-0.0267	0.3081	-0.0666	0.1473	-0.0443	-0.1309	-0.0159	0.0316	-0.2781	-61.195	4.755	-8.675
2	1.6801	-1.392	-0.9066	6.554	-0.4916	2.883	-0.0363	-0.0619	0.0065	-0.6923	0.0569	-0.0127	0.212	0.0342	-0.0205	-0.053	-0.0791	-0.1229	0.0005	-0.0618	-0.2061	-65.267	-21.374	1.111
3	1.8232	-0.8649	-0.898	5.1441	-0.5916	5.4515	-0.1872	0.0416	-0.0228	-0.416	0.0035	-0.0846	0.153	0.1012	0.1837	-0.4276	-0.1046	-0.0132	-0.1415	0.0119	-0.1291	-70.915	-29.679	27.366
4	1.2249	-0.8949	-0.3852	6.3197	-1.0054	6.0337	-0.0154	0.1215	0.1474	0.3613	-0.0846	-0.0117	-0.6453	0.3382	0.1	-0.4893	-0.0813	0.0376	-0.1833	0.0337	-0.1667	-73.844	-14.013	50.649
5	1.9384	1.7673	0.6472	6.9479	-0.2842	5.154	0.2662	-0.108	-0.0307	0.8867	-0.1205	0.0785	0.2911	0.0662	-0.1457	-0.2388	-0.0089	0.1506	-0.185	0.0001	-0.1797	-71.771	13.663	53.368
6	1.9112	2.6519	0.9047	7.0999	0.5956	4.0197	0.0535	0.1831	-0.116	0.3055	0.1522	0.0145	0.2345	0.2384	-0.2057	-0.4766	0.074	0.0584	-0.2364	-0.0132	-0.1803	-65.164	32.434	33.42
7	2.9875	3.1222	-1.1615	7.6579	-1.3579	4.9167	-0.0459	0.0579	-0.2478	-0.5168	0.1061	-0.2351	0.3166	0.1764	-0.0603	-0.2397	0.0395	-0.0656	-0.1654	0.0796	-0.2184	-61.049	28.795	5.789
8	3.0033	2.9161	0.9299	4.7547	2.241	5.8778	-0.1731	-0.0581	0.0266	-0.3755	-0.0285	-0.0886	-0.2314	-0.2266	0.2016	-0.3056	0.1019	0.072	-0.2057	-0.0157	-0.1435	-24.312	-24.727	8.649
9	2.3545	1.2084	-1.0495	3.5131	-0.0639	4.4206	-0.2278	0.2228	0.0387	-0.1598	-0.0048	0.1551	-0.1988	-0.2179	0.2325	-0.5385	0.098	-0.0744	-0.2004	0.085	-0.102	-30.242	-33.981	34.581
10	2.0262	0.7117	-0.9998	4.4675	0.8215	3.1636	0.2245	-0.1215	0.087	0.5283	-0.2033	0.2041	-0.2078	-0.103	-0.0212	-0.2336	0.0083	-0.0886	-0.0675	0.0658	-0.1916	-33.026	-19.228	58.386
11	2.4509	-0.6771	-2.0391	5.2173	-0.266	4.3405	-0.0138	-0.1285	0.0498	0.2797	0.0366	0.17	-0.0976	-0.0321	-0.0229	-0.1803	-0.1507	-0.1487	-0.0421	-0.0925	-0.1854	-30.747	8.522	62.011
12	1.3021	-1.1528	-0.6921	5.1594	0.6169	2.9108	0.0372	0.0319	-0.2713	-0.1316	-0.0667	0.2739	0.1816	-0.1581	0.0295	-0.463	-0.1319	-0.0866	-0.1003	-0.1196	-0.0658	-24.963	28.01	42.676
13	2.2552	-1.6714	-0.2231	7.9424	0.7755	4.256	0.1564	0.1219	0.181	-1.1334	-0.0626	-0.2591	-0.1322	-0.2124	-0.0938	-0.1264	-0.0743	0.1734	-0.1241	-0.0347	-0.1092	-18.925	25.007	15.307
14	2.2827	1.4282	0.6445	6.6715	-0.332	8.9943	0.0814	-0.0493	0.0953	-0.8145	0.0169	-0.1623	-0.7045	-0.351	-0.0982	0.0135	0.0563	0.2025	-0.1555	-0.035	-0.2227	-18.744	1.484	0.05

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	14 - 193
2	X-RAY DIFFRACTION	2	B	14 - 193
3	X-RAY DIFFRACTION	3	C	14 - 193
4	X-RAY DIFFRACTION	4	D	14 - 193
5	X-RAY DIFFRACTION	5	E	14 - 193
6	X-RAY DIFFRACTION	6	F	14 - 193
7	X-RAY DIFFRACTION	7	G	14 - 193
8	X-RAY DIFFRACTION	8	H	14 - 193
9	X-RAY DIFFRACTION	9	I	14 - 193
10	X-RAY DIFFRACTION	10	J	14 - 193
11	X-RAY DIFFRACTION	11	K	14 - 193
12	X-RAY DIFFRACTION	12	L	14 - 193
13	X-RAY DIFFRACTION	13	M	14 - 193
14	X-RAY DIFFRACTION	14	N	14 - 193

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