PDB-8r03: Staphylococcus aureus ClpP in complex with the natural product be...

ID or keywords:

Entry

Database: PDB / ID: 8r03

Title

Staphylococcus aureus ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.0 A resolution

Components

ATP-dependent Clp protease proteolytic subunit

Keywords

HYDROLASE / anti-virulence / caseinolytic protease / inhibitor / natural product / mode of action

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

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Illigmann, A. / Vielberg, M.-T. / Lakemeyer, M. / Wolf, F. / Staudt, N. / Dema, T. / Stange, P. / Liebhart, E. / Kuttenlochner, W. / Kulik, A. ...

Funding support

Germany, 1items

Citation

Journal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Structure of Staphylococcus aureus ClpP Bound to the Covalent Active-Site Inhibitor Cystargolide A.
Authors: Illigmann, A. / Vielberg, M.T. / Lakemeyer, M. / Wolf, F. / Dema, T. / Stange, P. / Kuttenlochner, W. / Liebhart, E. / Kulik, A. / Staudt, N.D. / Malik, I. / Grond, S. / Sieber, S.A. / ...

History

Deposition	Oct 30, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2023	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2	Jan 17, 2024	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3	Jan 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4	Oct 16, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8r03.cif.gz	1 MB	Display	PDBx/mmCIF format
PDB format	pdb8r03.ent.gz	862.1 KB	Display	PDB format
PDBx/mmJSON format	8r03.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8r03_validation.pdf.gz	4.6 MB	Display	wwPDB validaton report
Full document	8r03_full_validation.pdf.gz	4.5 MB	Display
Data in XML	8r03_validation.xml.gz	103.1 KB	Display
Data in CIF	8r03_validation.cif.gz	140.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r0/8r03 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/8r03	HTTPS FTP

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Related structure data

Related structure data	8ollC 8olrC 8r04C 8r05C 3v5e C: citing same article (ref.)
Similar structure data	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

B: ATP-dependent Clp protease proteolytic subunit

C: ATP-dependent Clp protease proteolytic subunit

D: ATP-dependent Clp protease proteolytic subunit

E: ATP-dependent Clp protease proteolytic subunit

F: ATP-dependent Clp protease proteolytic subunit

G: ATP-dependent Clp protease proteolytic subunit

H: ATP-dependent Clp protease proteolytic subunit

I: ATP-dependent Clp protease proteolytic subunit

J: ATP-dependent Clp protease proteolytic subunit

K: ATP-dependent Clp protease proteolytic subunit

L: ATP-dependent Clp protease proteolytic subunit

M: ATP-dependent Clp protease proteolytic subunit

N: ATP-dependent Clp protease proteolytic subunit

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	110.620, 105.740, 150.370
Angle α, β, γ (deg.)	90.00, 102.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 21549.465 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: clpP, SAOUHSC_00790 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G036, endopeptidase Clp
#2: Chemical	ChemComp-VSZ / Cystargolide A (bound) / (2S,3S)-2-[[(2S)-2-[[(2R,3S)-3-methanoyl-4-methyl-2-oxidanyl-pentanoyl]amino]-3-methyl-butanoyl]amino]-3-methyl-pentanoic acid Mass: 372.456 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C₁₈H₃₂N₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1323 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.85 Å³/Da / Density % sol: 56.86 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammoniumcitrate, 20% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→30 Å / Num. obs: 219187 / % possible obs: 96.1 % / Redundancy: 2.9 % / R_merge(I) obs: 0.065 / Net I/σ(I): 12.8
Reflection shell	Resolution: 2→2.1 Å / Redundancy: 3 % / R_merge(I) obs: 0.624 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 30619 / % possible all: 99

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.949 / SU B: 7.622 / SU ML: 0.093 / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20291	10957	5 %	RANDOM
R_work	0.1595	-	-	-
obs	0.16169	208176	96.12 %	-

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: 30.57 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.23 Å²	-0 Å²	-0.13 Å²
2-	-	-0.64 Å²	0 Å²
3-	-	-	-0.49 Å²

Refinement step

Cycle: 1 / Resolution: 2→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19968	0	52	1323	21343

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.013	20262
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	19932
X-RAY DIFFRACTION	r_angle_refined_deg	1.298	1.641	27348
X-RAY DIFFRACTION	r_angle_other_deg	1.216	1.581	45871
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.129	5	2513
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.817	23.611	1008
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.19	15	3634
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.22	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.056	0.2	2893
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	22782
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4222
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
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
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
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	1.91	2.273	10136
X-RAY DIFFRACTION	r_mcbond_other	1.909	2.273	10135
X-RAY DIFFRACTION	r_mcangle_it	2.485	3.396	12621
X-RAY DIFFRACTION	r_mcangle_other	2.485	3.396	12622
X-RAY DIFFRACTION	r_scbond_it	2.609	2.771	10126
X-RAY DIFFRACTION	r_scbond_other	2.609	2.771	10127
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.243	3.994	14728
X-RAY DIFFRACTION	r_long_range_B_refined	3.778	29.126	22373
X-RAY DIFFRACTION	r_long_range_B_other	3.694	28.845	22106
X-RAY DIFFRACTION	r_rigid_bond_restr	1.157	3	40194
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2→2.052 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.256	832	-
R_work	0.213	15803	-
obs	-	-	99.4 %

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	0.1817	-0.1042	0.2562	0.1849	0.103	0.9516	-0.0687	0.0031	-0.0278	0.015	0.041	0.0086	-0.1526	0.0742	0.0277	0.0323	-0.0031	0.0086	0.0842	-0.0064	0.0767	12.021	2.3318	27.751
2	0.3014	-0.1069	-0.1322	0.1379	-0.1249	0.6361	-0.002	-0.0197	-0.0262	0.0563	0.0166	-0.0099	-0.0792	0.0433	-0.0146	0.049	0.0035	-0.0036	0.0808	-0.0143	0.0413	6.0973	1.9691	54.3122
3	0.244	-0.0346	-0.0143	0.4161	-0.0356	0.0209	-0.0113	0.0167	-0.0053	0.0665	-0	0.0144	0.0026	0.0255	0.0114	0.0763	0.0058	-0.0012	0.0806	-0.0085	0.034	-6.9377	-16.7893	68.3185
4	0.2439	0.0745	0.1244	0.2635	0.2028	0.2124	0.0231	-0.0041	-0.0251	0.0345	-0.0345	0.028	0.0015	-0.0004	0.0115	0.0787	0.0085	0.0107	0.0687	0.0103	0.0362	-17.7419	-39.699	59.625
5	0.2421	0.0012	0.0254	0.1443	-0.1151	0.3985	0.0271	0.0102	0.0118	0.0227	-0.0313	0.0195	0.0644	0.022	0.0042	0.0778	0.0191	0.0029	0.0443	0.003	0.0571	-17.9247	-49.8135	34.9611
6	0.1343	0.131	-0.1076	0.2776	-0.1578	0.1453	-0.031	-0.0034	0.0181	-0.0158	0.0199	0.0077	0.0681	0.0104	0.0111	0.0682	0.0268	0.0114	0.0525	-0.0053	0.0709	-7.3643	-39.4518	12.5161
7	0.0399	0.1006	0.0364	0.4226	0.1536	0.2816	-0.0226	-0.0201	0.0119	-0.0392	0.0275	-0.0119	0.0271	0.0371	-0.0049	0.0306	0.0247	0.0146	0.0644	-0.0131	0.0927	5.8612	-16.3511	9.56
8	0.1124	0.0055	0.1519	0.6022	0.2056	0.2774	-0.0057	-0.0062	0.0027	0.1298	-0.0246	0.0969	0.0324	-0.0402	0.0303	0.0358	0.0004	0.0426	0.0959	-0.0133	0.0854	-56.6964	-15.6872	53.062
9	0.3084	0.1648	0.0544	0.5795	-0.2585	0.2161	-0.0152	0.0202	0.0084	0.081	-0.0381	0.0025	-0.0329	-0.0039	0.0533	0.0658	0.0143	0.0508	0.0996	-0.0179	0.0794	-45.5625	7.6032	59.3731
10	0.1937	0.0704	-0.0615	0.2163	-0.3897	0.8297	-0.013	0.0172	0.0131	0.0578	-0.0398	0.0157	-0.0961	0.0631	0.0528	0.0514	0.0148	0.0149	0.0885	-0.0166	0.0617	-32.6236	24.9084	42.9336
11	0.2763	0.0002	-0.1336	0.2151	0.2253	0.3628	0.0077	-0.0093	-0.0172	-0.0168	-0.0078	0.0173	-0.0579	0.0072	0	0.0436	0.0167	-0.0085	0.0598	0.007	0.0767	-28.2241	22.7309	16.7257
12	0.0804	0.095	-0.0339	0.4889	0.0064	0.1842	0.0034	-0.0097	-0.0161	-0.0577	0.0044	-0.006	-0.0358	-0.0227	-0.0078	0.0272	0.0042	-0.0285	0.0598	0.012	0.0901	-35.0287	3.1379	-0.1612
13	0.1753	-0.1119	-0.0748	0.4053	-0.1873	0.2793	-0.0322	0.0048	-0.0161	-0.0198	-0.0021	0.0435	0.0135	-0.0056	0.0343	0.0256	-0.007	-0.0355	0.0565	-0.0129	0.1138	-48.6557	-19.3985	5.5276
14	0.1747	-0.2027	0.0377	0.3205	0.1163	0.4345	-0.0252	-0.0216	-0.0273	0.0273	-0.0076	0.0753	0.027	-0.0461	0.0328	0.0142	-0.0053	-0.0031	0.0739	-0.0201	0.125	-58.3428	-27.7661	28.8815

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	4 - 195
2	X-RAY DIFFRACTION	2	B	4 - 193
3	X-RAY DIFFRACTION	3	C	5 - 194
4	X-RAY DIFFRACTION	4	D	4 - 194
5	X-RAY DIFFRACTION	5	E	4 - 195
6	X-RAY DIFFRACTION	6	F	4 - 195
7	X-RAY DIFFRACTION	7	G	4 - 194
8	X-RAY DIFFRACTION	8	H	4 - 192
9	X-RAY DIFFRACTION	9	I	4 - 195
10	X-RAY DIFFRACTION	10	J	4 - 193
11	X-RAY DIFFRACTION	11	K	4 - 194
12	X-RAY DIFFRACTION	12	L	4 - 195
13	X-RAY DIFFRACTION	13	M	4 - 194
14	X-RAY DIFFRACTION	14	N	4 - 194

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