PDB-6hwn: Structure of Thermus thermophilus ClpP in complex with a tripeptide.

ID or keywords:

Entry

Database: PDB / ID: 6hwn

Title

Structure of Thermus thermophilus ClpP in complex with a tripeptide.

Components

ATP-dependent Clp protease proteolytic subunit
Unknown tripeptide

Keywords

HYDROLASE / complex / activator

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 / cytoplasm
Similarity search - Function

Biological species

Thermus thermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.95 Å

Authors

Felix, J. / Schanda, P. / Fraga, H. / Morlot, C.

Funding support

France, 3items

Citation

Journal: Sci Adv / Year: 2019
Title: Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors.
Authors: Felix, J. / Weinhaupl, K. / Chipot, C. / Dehez, F. / Hessel, A. / Gauto, D.F. / Morlot, C. / Abian, O. / Gutsche, I. / Velazquez-Campoy, A. / Schanda, P. / Fraga, H.

History

Deposition	Oct 12, 2018	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	Sep 25, 2019	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Jan 24, 2024	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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6hwn.cif.gz	528.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6hwn.ent.gz	438.1 KB	Display	PDB format
PDBx/mmJSON format	6hwn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hw/6hwn ftp://data.pdbj.org/pub/pdb/validation_reports/hw/6hwn	HTTPS FTP

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Related structure data

Related structure data	6hwmC 3ktiS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5g1s-2 5g1s-1 3p2l-1 5c90-d 7950 5dzk-1 6mx2-d 3tt7-1 3v5i-1 5dzk-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: ATP-dependent Clp protease proteolytic subunit

H: Unknown tripeptide

B: ATP-dependent Clp protease proteolytic subunit

I: Unknown tripeptide

C: ATP-dependent Clp protease proteolytic subunit

J: Unknown tripeptide

D: ATP-dependent Clp protease proteolytic subunit

K: Unknown tripeptide

E: ATP-dependent Clp protease proteolytic subunit

L: Unknown tripeptide

F: ATP-dependent Clp protease proteolytic subunit

M: Unknown tripeptide

G: ATP-dependent Clp protease proteolytic subunit

N: Unknown tripeptide

hetero molecules

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

1

A: ATP-dependent Clp protease proteolytic subunit

H: Unknown tripeptide

B: ATP-dependent Clp protease proteolytic subunit

I: Unknown tripeptide

C: ATP-dependent Clp protease proteolytic subunit

J: Unknown tripeptide

D: ATP-dependent Clp protease proteolytic subunit

K: Unknown tripeptide

E: ATP-dependent Clp protease proteolytic subunit

L: Unknown tripeptide

F: ATP-dependent Clp protease proteolytic subunit

M: Unknown tripeptide

G: ATP-dependent Clp protease proteolytic subunit

N: Unknown tripeptide

hetero molecules

A: ATP-dependent Clp protease proteolytic subunit

H: Unknown tripeptide

B: ATP-dependent Clp protease proteolytic subunit

I: Unknown tripeptide

C: ATP-dependent Clp protease proteolytic subunit

J: Unknown tripeptide

D: ATP-dependent Clp protease proteolytic subunit

K: Unknown tripeptide

E: ATP-dependent Clp protease proteolytic subunit

L: Unknown tripeptide

F: ATP-dependent Clp protease proteolytic subunit

M: Unknown tripeptide

G: ATP-dependent Clp protease proteolytic subunit

N: Unknown tripeptide

hetero molecules

defined by author&software
Evidence: gel filtration
326 kDa, 28 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	105.976, 162.786, 107.948
Angle α, β, γ (deg.)	90.00, 116.34, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	F-421- HOH

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 22763.105 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: clpP, TT_C0250 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72L15, endopeptidase Clp
#2: Protein/peptide	Unknown tripeptide Mass: 273.330 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Details: We observe a continuous stretch of electron density near the active site serine (Ser97) of each TtClpP monomer, which based on its shape, suggests the presence of a tripeptide. Due to the ...Details: We observe a continuous stretch of electron density near the active site serine (Ser97) of each TtClpP monomer, which based on its shape, suggests the presence of a tripeptide. Due to the unknown nature of the proposed tripeptide, we have built it in the electron density as tri-L-alanine. Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 628 / 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: 2.62 Å³/Da / Density % sol: 53.03 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.8 / Details: 100 mM Sodium acetate pH 4.8 and 30% PEG 400.

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
Detector	Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.966 Å / Relative weight: 1
Reflection	Resolution: 1.95→46.59 Å / Num. obs: 118066 / % possible obs: 99.25 % / Redundancy: 5.3 % / CC_1/2: 0.999 / R_rim(I) all: 0.078 / Net I/σ(I): 13.06
Reflection shell	Resolution: 1.95→1.97222 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.56 / Num. unique obs: 11696 / CC_1/2: 0.646 / R_rim(I) all: 1.093 / % possible all: 98.58

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Processing

Software

Name	Version	Classification
PHENIX	(1.13_2998: ???)	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3KTI

3kti

Resolution: 1.95→46.587 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2109	11804	10 %
R_work	0.1858	-	-
obs	0.1883	118032	99.26 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.95→46.587 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10093	0	119	631	10843

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	10575
X-RAY DIFFRACTION	f_angle_d	0.956	14352
X-RAY DIFFRACTION	f_dihedral_angle_d	19.591	3889
X-RAY DIFFRACTION	f_chiral_restr	0.068	1676
X-RAY DIFFRACTION	f_plane_restr	0.006	1851

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 (%)
1.95-1.9722	0.3679	389	0.3443	3504	X-RAY DIFFRACTION	98
1.9722-1.9954	0.3648	387	0.3071	3482	X-RAY DIFFRACTION	99
1.9954-2.0197	0.3139	393	0.2819	3541	X-RAY DIFFRACTION	99
2.0197-2.0453	0.3301	386	0.2773	3474	X-RAY DIFFRACTION	99
2.0453-2.0722	0.2779	395	0.2433	3558	X-RAY DIFFRACTION	99
2.0722-2.1006	0.2783	388	0.2373	3493	X-RAY DIFFRACTION	99
2.1006-2.1306	0.2595	390	0.2284	3516	X-RAY DIFFRACTION	99
2.1306-2.1624	0.255	393	0.226	3533	X-RAY DIFFRACTION	99
2.1624-2.1962	0.2528	389	0.2246	3503	X-RAY DIFFRACTION	99
2.1962-2.2322	0.2284	390	0.2044	3507	X-RAY DIFFRACTION	99
2.2322-2.2707	0.233	394	0.1942	3547	X-RAY DIFFRACTION	99
2.2707-2.3119	0.2329	396	0.1967	3561	X-RAY DIFFRACTION	99
2.3119-2.3564	0.2356	392	0.1925	3523	X-RAY DIFFRACTION	99
2.3564-2.4045	0.229	392	0.1921	3529	X-RAY DIFFRACTION	99
2.4045-2.4568	0.2248	391	0.1855	3524	X-RAY DIFFRACTION	99
2.4568-2.5139	0.217	395	0.1875	3548	X-RAY DIFFRACTION	99
2.5139-2.5768	0.2266	395	0.1867	3559	X-RAY DIFFRACTION	99
2.5768-2.6465	0.2318	393	0.1842	3533	X-RAY DIFFRACTION	99
2.6465-2.7243	0.2354	391	0.192	3520	X-RAY DIFFRACTION	99
2.7243-2.8123	0.2269	396	0.1955	3566	X-RAY DIFFRACTION	100
2.8123-2.9127	0.2159	392	0.1764	3526	X-RAY DIFFRACTION	100
2.9127-3.0294	0.2037	400	0.1818	3598	X-RAY DIFFRACTION	100
3.0294-3.1672	0.1978	393	0.1909	3540	X-RAY DIFFRACTION	100
3.1672-3.3341	0.2142	395	0.1855	3555	X-RAY DIFFRACTION	100
3.3341-3.543	0.2198	395	0.1868	3555	X-RAY DIFFRACTION	100
3.543-3.8164	0.1844	397	0.1679	3573	X-RAY DIFFRACTION	100
3.8164-4.2002	0.1723	398	0.1576	3584	X-RAY DIFFRACTION	100
4.2002-4.8075	0.1679	397	0.1512	3568	X-RAY DIFFRACTION	100
4.8075-6.0548	0.2045	399	0.1914	3590	X-RAY DIFFRACTION	100
6.0548-46.5999	0.1935	403	0.1757	3618	X-RAY DIFFRACTION	100

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	1.2481	-0.1066	0.3461	1.3789	-0.3388	0.9797	-0.0317	0.2411	-0.0027	-0.1691	0.0146	-0.1074	-0.0384	-0.0788	-0	0.3711	-0.0138	0.0851	0.3949	-0.0174	0.2065	-8.1856	-16.9886	13.8197
2	0.0206	-0.0468	0.0041	0.4914	-0.1023	0.0385	0.0484	-0.0312	-0.0517	0.0345	0.0345	-0.0291	-0.0108	0.0037	-0.0002	1.1435	-0.0881	-0.1026	0.4248	-0.045	0.8392	-4.4024	-23.0716	25.0183
3	1.2676	-0.1507	-0.0562	0.9645	-0.5298	1.4211	-0.0151	0.2414	-0.1724	-0.1753	0.043	-0.0661	-0.0045	-0.0661	0	0.3902	-0.0711	0.0804	0.4007	-0.1108	0.287	-14.2134	-43.1174	16.8217
4	0.1668	0.1415	-0.1719	0.1446	-0.1339	0.1904	0.0616	-0.05	-0.0319	0.0674	0.0649	-0.0016	0.0346	0.0021	-0.0001	0.676	-0.3875	-0.0011	1.1694	-0.0413	1.0205	-13.7496	-45.2271	30.0346
5	1.0663	-0.1124	-0.0262	1.0312	-0.188	1.2687	-0.0959	0.1854	-0.2139	-0.2007	0.1528	0.0137	0.0343	-0.0186	-0	0.3293	-0.0803	0.0099	0.3725	-0.0552	0.343	-35.7277	-53.8602	27.8853
6	0.1842	-0.0879	-0.1906	0.1399	0.0907	0.1965	0.0343	-0.0564	-0.0157	0.0634	0.0059	0.0001	-0.0088	-0.0249	-0.0025	0.4142	0.036	0.0408	1.1497	-0.1342	0.688	-34.88	-50.8791	41.1873
7	0.7768	0.1952	0.0024	1.3961	0.5703	1.6514	-0.1103	0.0855	-0.0806	-0.1089	-0.0086	0.2141	-0.0599	-0.0319	-0	0.26	-0.0045	-0.0257	0.2442	-0.0188	0.4145	-56.519	-41.6411	39.5769
8	0.0116	-0.0208	-0.0164	0.1231	0.0508	0.0301	-0.0653	-0.1172	0.0294	0.0599	-0.0502	-0.0362	-0.0727	0.0054	0	1.018	0.1878	-0.0408	0.5811	0.0627	0.9697	-51.7856	-35.5165	50.0123
9	1.3647	0.3123	0.26	0.9409	0.4166	1.2702	-0.019	0.1098	-0.0968	-0.073	0.027	0.1167	-0.0093	0.0304	0	0.2431	0.0078	-0.0376	0.2281	0.0049	0.4005	-60.9496	-15.4534	41.6671
10	0.0555	0.0721	0.0073	0.1212	0.0085	0.0019	0.0169	-0.0544	-0.0168	0.035	-0.0037	0.043	-0.1307	0.0406	0	0.6832	-0.1549	0.0271	0.4842	0.1324	0.8793	-51.762	-10.9334	49.7974
11	1.2378	0.2962	0.2115	0.9779	0.28	0.7329	-0.0038	0.1965	0.1112	-0.101	0.0589	0.0928	-0.0198	0.0055	0	0.2701	-0.0057	-0.0251	0.2658	0.0718	0.3445	-45.6796	4.7814	33.4871
12	0.4963	0.0574	-0.0673	0.0345	-0.0183	0.0126	-0.0773	-0.0372	0.0077	0.0918	-0.0111	0.0485	-0.0393	0.159	0.0002	0.6645	-0.0313	-0.0451	0.9158	0.0703	0.7364	-35.0748	4.3936	41.0666
13	1.7968	-0.1646	0.5769	1.3219	-0.2008	1.1191	-0.0092	0.28	0.1807	-0.1319	-0.0013	-0.0058	0.0095	0.0425	0	0.312	-0.0002	0.0079	0.3253	0.0589	0.2442	-22.0837	4.4163	21.3552
14	0.1271	-0.0885	-0.0115	0.0766	0.0018	0.0027	-0.0014	-0.0201	0.0345	0.0874	0.0006	0.0048	0.0541	0.1462	-0	0.6758	0.2832	0.0099	0.9023	-0.1205	0.9231	-13.9622	-0.8747	29.9267

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	(chain 'A' and resid 2 through 195)
2	X-RAY DIFFRACTION	2	(chain 'H' and resid 1 through 3)
3	X-RAY DIFFRACTION	3	(chain 'B' and resid 2 through 193)
4	X-RAY DIFFRACTION	4	(chain 'I' and resid 1 through 3)
5	X-RAY DIFFRACTION	5	(chain 'C' and resid 2 through 193)
6	X-RAY DIFFRACTION	6	(chain 'J' and resid 1 through 3)
7	X-RAY DIFFRACTION	7	(chain 'D' and resid 2 through 195)
8	X-RAY DIFFRACTION	8	(chain 'K' and resid 1 through 3)
9	X-RAY DIFFRACTION	9	(chain 'E' and resid 3 through 194)
10	X-RAY DIFFRACTION	10	(chain 'L' and resid 1 through 3)
11	X-RAY DIFFRACTION	11	(chain 'F' and resid 2 through 193)
12	X-RAY DIFFRACTION	12	(chain 'M' and resid 1 through 3)
13	X-RAY DIFFRACTION	13	(chain 'G' and resid 2 through 193)
14	X-RAY DIFFRACTION	14	(chain 'N' and resid 1 through 3)

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