PDB-8r05: Photorhabdus lamondii ClpP in complex with the natural product be...

ID or keywords:

Entry

Database: PDB / ID: 8r05

Title

Photorhabdus lamondii ClpP in complex with the natural product beta-lactone inhibitor Cystargolide A at 2.5 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

Photorhabdus laumondii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.5 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	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.title / _citation.year / _citation_author.name
Revision 1.2	Jan 24, 2024	Group: Database references / Category: citation / citation_author Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3	Nov 20, 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	8r05.cif.gz	1008.9 KB	Display	PDBx/mmCIF format
PDB format	pdb8r05.ent.gz	847.1 KB	Display	PDB format
PDBx/mmJSON format	8r05.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/r0/8r05 ftp://data.pdbj.org/pub/pdb/validation_reports/r0/8r05	HTTPS FTP

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Related structure data

Related structure data	8ollC 8olrC 8r03C 8r04C 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

332 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)	96.070, 177.940, 102.840
Angle α, β, γ (deg.)	90.00, 112.16, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 23333.803 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Photorhabdus laumondii (bacteria) / Gene: clpP, plu3869 / Plasmid: pET-Duet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7N0L3, 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: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.5 Å³/Da / Density % sol: 50.79 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 20% PEG 4000, 10% isopropanole

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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: Apr 7, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.5→30 Å / Num. obs: 107872 / % possible obs: 97.7 % / Redundancy: 3.1 % / R_merge(I) obs: 0.082 / Net I/σ(I): 10.9
Reflection shell	Resolution: 2.5→2.6 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.667 / Mean I/σ(I) obs: 2 / Num. unique obs: 11693 / % possible all: 95.9

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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: 2.5→30 Å / Cor.coef. F_o:F_c: 0.955 / Cor.coef. F_o:F_c free: 0.931 / SU B: 24.62 / SU ML: 0.227 / Cross valid method: THROUGHOUT / ESU R Free: 0.269 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23413	5391	5 %	RANDOM
R_work	0.18652	-	-	-
obs	0.18888	102428	97.78 %	-

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: 56.965 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.47 Å²	0 Å²	1.58 Å²
2-	-	-3.77 Å²	0 Å²
3-	-	-	2.21 Å²

Refinement step

Cycle: 1 / Resolution: 2.5→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20456	0	0	101	20557

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.013	20780
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	20388
X-RAY DIFFRACTION	r_angle_refined_deg	1.163	1.643	27996
X-RAY DIFFRACTION	r_angle_other_deg	1.041	1.578	46932
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.842	5	2547
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.92	22.16	1051
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.911	15	3788
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.203	15	129
X-RAY DIFFRACTION	r_chiral_restr	0.038	0.2	2855
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	23064
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	4470
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	2.29	5.014	10266
X-RAY DIFFRACTION	r_mcbond_other	2.29	5.014	10265
X-RAY DIFFRACTION	r_mcangle_it	3.189	7.512	12787
X-RAY DIFFRACTION	r_mcangle_other	3.189	7.512	12788
X-RAY DIFFRACTION	r_scbond_it	2.257	5.46	10514
X-RAY DIFFRACTION	r_scbond_other	2.256	5.46	10515
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.148	8.047	15210
X-RAY DIFFRACTION	r_long_range_B_refined	4.216	58.693	21214
X-RAY DIFFRACTION	r_long_range_B_other	4.198	58.682	21207
X-RAY DIFFRACTION	r_rigid_bond_restr	0.509	3	41168
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.564 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.348	387	-
R_work	0.303	7357	-
obs	-	-	95.87 %

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	0.1731	0.1062	0.024	0.2437	0.0438	0.1396	-0.0045	0.0683	-0.0818	-0.0315	-0.0028	-0.0724	0.037	0.0473	0.0073	0.0744	-0.0018	0.0628	0.0972	-0.0677	0.114	55.66	94.922	51.172
2	0.2425	0.2218	0.0292	0.3242	0.2142	0.8158	-0.0117	-0.0378	-0.1163	-0.0174	-0.0181	-0.0857	0.0284	-0.0026	0.0298	0.0593	0.0162	0.0275	0.0191	0.0037	0.1704	57.449	84.936	75.491
3	0.1873	0.0362	0.0033	0.3824	0.1458	0.2096	-0.0034	-0.0712	-0.1156	-0.0219	-0.0133	-0.0215	-0.0157	-0.0241	0.0167	0.0679	0.0081	0.0047	0.0359	0.0382	0.1449	37.194	82.629	92.584
4	0.2538	-0.0634	0.1005	0.5743	0.1928	0.1335	0.0141	-0.0478	-0.0583	-0.0231	0.0003	0.0173	-0.005	-0.0199	-0.0143	0.0816	-0.0112	0.0268	0.0653	0.0301	0.0978	12.059	90.865	89.688
5	0.2416	-0.0073	-0.0085	0.6093	0.0237	0.1359	-0.0132	0.0431	-0.0626	-0.0033	0.0075	0.0445	-0.0196	0.0073	0.0057	0.0682	-0.0084	0.007	0.0892	-0.0118	0.086	0.76	103.564	69.054
6	0.464	0.1781	-0.056	0.7536	-0.0342	0.0095	-0.0433	0.1511	-0.006	-0.0512	0.0433	0.0207	0.0204	-0.0128	0.0001	0.0966	-0.0109	-0.0017	0.1456	-0.0185	0.0035	11.695	110.74	46.217
7	0.3636	0.2438	0.078	0.5389	0.0525	0.0203	-0.0252	0.2026	-0.0629	-0.026	0.0397	-0.052	0.0026	0.0459	-0.0145	0.0947	-0.0293	0.0406	0.1651	-0.0445	0.0275	36.802	107.239	38.596
8	0.3968	-0.0145	-0.0486	0.5004	0.068	0.0194	0.0078	-0.1396	0.0495	0.0269	0.004	-0.0415	0.0178	0.024	-0.0117	0.0695	-0.0033	-0.0247	0.1432	-0.0226	0.04	50.891	123.094	110.59
9	0.1952	-0.0337	-0.181	0.2963	0.0783	0.2429	0.0037	-0.0408	0.0469	0.003	-0.0106	-0.0596	0.0017	0.0325	0.0069	0.029	0.0039	-0.0149	0.0861	-0.0273	0.1317	68.9	126.917	91.829
10	0.1129	0.0829	0.0266	0.248	0.1399	0.2442	-0.0128	0.0406	0.0808	-0.0258	0.0005	-0.0506	-0.0021	0.003	0.0124	0.0436	-0.0206	0.0177	0.0707	0.0126	0.1776	66.578	139.027	69.288
11	0.4164	0.0579	0.1189	0.3161	0.1641	0.2294	-0.0233	0.0755	0.1683	-0.0403	0.0054	-0.0569	0.0097	-0.0144	0.0179	0.0696	-0.0142	0.0173	0.0479	0.062	0.1362	45.966	149.079	56.708
12	0.3112	0.1509	0.0262	0.4115	0.037	0.1253	-0.0249	0.0206	0.0933	-0.0224	-0.004	-0.0067	-0.0014	-0.0294	0.0289	0.0782	-0.0003	-0.0039	0.0412	0.0376	0.1262	21.561	151.244	66.864
13	0.1737	0.2365	0.1047	0.7703	-0.0587	0.2085	-0.0185	-0.0363	0.0497	0.018	0.0187	0.0205	0.0034	-0.0326	-0.0002	0.0601	0.0295	0.0128	0.0659	-0.0288	0.1316	12.519	142.968	90.282
14	0.3776	0.0234	0.1081	0.5437	-0.0583	0.0676	0.028	-0.1144	0.0367	0.0648	-0.0101	0.0194	-0.0031	0.0213	-0.0178	0.0657	-0.0058	0.0227	0.1366	-0.0567	0.0383	25.566	130.278	109.744

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 206
2	X-RAY DIFFRACTION	2	B	17 - 205
3	X-RAY DIFFRACTION	3	C	16 - 206
4	X-RAY DIFFRACTION	4	D	17 - 206
5	X-RAY DIFFRACTION	5	E	17 - 206
6	X-RAY DIFFRACTION	6	F	17 - 206
7	X-RAY DIFFRACTION	7	G	16 - 206
8	X-RAY DIFFRACTION	8	H	17 - 206
9	X-RAY DIFFRACTION	9	I	15 - 206
10	X-RAY DIFFRACTION	10	J	17 - 206
11	X-RAY DIFFRACTION	11	K	17 - 206
12	X-RAY DIFFRACTION	12	L	17 - 207
13	X-RAY DIFFRACTION	13	M	17 - 206
14	X-RAY DIFFRACTION	14	N	17 - 206

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