PDB-6pka: Structure of ClpP from Staphylococcus aureus in complex with urea...

ID or keywords:

Entry

Database: PDB / ID: 6pka

Title

Structure of ClpP from Staphylococcus aureus in complex with ureadepsipeptide

Components

ATP-dependent Clp protease proteolytic subunit
OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

Keywords

HYDROLASE/ANTIBIOTIC / ClpP ADEP / ANTIBIOTIC / HYDROLASE-ANTIBIOTIC complex

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)
synthetic construct (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.25 Å

Authors

Griffith, E.C. / Lee, R.E.

Funding support

United States, 1items

Citation

Journal: Acs Infect Dis. / Year: 2019
Title: Ureadepsipeptides as ClpP Activators.
Authors: Griffith, E.C. / Zhao, Y. / Singh, A.P. / Conlon, B.P. / Tangallapally, R. / Shadrick, W.R. / Liu, J. / Wallace, M.J. / Yang, L. / Elmore, J.M. / Li, Y. / Zheng, Z. / Miller, D.J. / ...

History

Deposition	Jun 28, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 6, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2	Dec 18, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 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_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6pka.cif.gz	519 KB	Display	PDBx/mmCIF format
PDB format	pdb6pka.ent.gz	423.7 KB	Display	PDB format
PDBx/mmJSON format	6pka.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6pka_validation.pdf.gz	564 KB	Display	wwPDB validaton report
Full document	6pka_full_validation.pdf.gz	588.9 KB	Display
Data in XML	6pka_validation.xml.gz	95.1 KB	Display
Data in CIF	6pka_validation.cif.gz	137 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pk/6pka ftp://data.pdbj.org/pub/pdb/validation_reports/pk/6pka	HTTPS FTP

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Related structure data

Related structure data	5vz2C 5w18C 6pmdC 3staS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5vz2-d 5w18-d 6pmd-d 6nah-1 6nah-2 6l40-d 4jcr-d 6nb1-d 6naw-d 6w9t-1 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

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

I: 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

S: ATP-dependent Clp protease proteolytic subunit

T: ATP-dependent Clp protease proteolytic subunit

H: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

J: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

O: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

P: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

Q: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

R: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

U: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

V: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

X: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

Y: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

Z: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

a: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

b: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

c: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide

328 kDa, 28 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: equilibrium centrifugation

Unit cell

Length a, b, c (Å)	94.957, 126.681, 146.776
Angle α, β, γ (deg.)	90.000, 93.360, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 4 - 192 / Label seq-ID: 4 - 192

NCS ensembles :

#1: Protein	ATP-dependent Clp protease proteolytic subunit / Endopeptidase Clp Mass: 22607.686 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria) Strain: NCTC 8325 / Gene: clpP, SAOUHSC_00790 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2G036, endopeptidase Clp
#2: Protein/peptide	OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide Type: Oligopeptide / Class: Antibiotic / Mass: 811.872 Da / Num. of mol.: 14 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: OO1-WFP-SER-PRO-YCP-ALA-MP8 ureadepsipeptide
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1100 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.78 Å³/Da / Density % sol: 55.83 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M NaOAc pH 4.5, 18-35% MPD, and 0.02 M CaCl2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 22-ID / Wavelength: 1 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 2, 2019

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.25→50 Å / Num. obs: 160858 / % possible obs: 97.5 % / Redundancy: 4.2 % / R_merge(I) obs: 0.205 / R_pim(I) all: 0.11 / R_rim(I) all: 0.234 / Χ²: 0.969 / Net I/σ(I): 7.3 / Num. measured all: 672138

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.25-2.29	4.4	0.663	8058	0.656	0.344	0.751	0.499	97.8
2.29-2.33	4.3	0.625	8110	0.66	0.324	0.708	0.514	97.8
2.33-2.38	4.3	0.581	7975	0.685	0.306	0.66	0.535	97.8
2.38-2.42	4.1	0.517	7986	0.707	0.279	0.591	0.576	97.4
2.42-2.48	3.8	0.482	7934	0.703	0.272	0.557	0.614	96.9
2.48-2.53	4.1	0.434	7956	0.753	0.236	0.498	0.644	96.4
2.53-2.6	4.5	0.4	7999	0.831	0.204	0.452	0.667	97
2.6-2.67	4.7	0.37	7969	0.865	0.185	0.416	0.736	97.1
2.67-2.75	4.6	0.329	8001	0.852	0.166	0.37	0.807	97
2.75-2.83	4.5	0.3	7973	0.873	0.154	0.339	0.872	96.9
2.83-2.94	4.4	0.268	8001	0.876	0.139	0.304	0.921	97
2.94-3.05	4.2	0.239	7998	0.891	0.126	0.272	1.051	97
3.05-3.19	4.1	0.219	8044	0.905	0.117	0.25	1.091	97.6
3.19-3.36	3.9	0.194	7975	0.915	0.107	0.223	1.243	97.3
3.36-3.57	3.5	0.176	7976	0.855	0.105	0.206	1.46	96.5
3.57-3.85	3.7	0.157	8061	0.925	0.091	0.183	1.405	97.5
3.85-4.23	4.2	0.151	8131	0.945	0.082	0.173	1.476	98.3
4.23-4.85	4	0.142	8109	0.948	0.077	0.162	1.435	97.7
4.85-6.1	4.1	0.154	8241	0.946	0.082	0.175	1.503	99.1
6.1-50	4.2	0.172	8361	0.957	0.086	0.193	1.623	99.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	4.59 Å	40.58 Å
Translation	4.59 Å	40.58 Å

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0222	refinement
HKL-2000		data scaling
PHASER	2.8.2	phasing
PDB_EXTRACT	3.24	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3STA

3sta

Resolution: 2.25→40.61 Å / Cor.coef. F_o:F_c: 0.927 / Cor.coef. F_o:F_c free: 0.913 / SU B: 5.522 / SU ML: 0.139 / SU R Cruickshank DPI: 0.2474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.247 / ESU R Free: 0.187
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2188	8139	5.1 %	RANDOM
R_work	0.1944	-	-	-
obs	0.1956	152696	96.98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso max: 89.64 Å² / B_iso mean: 29.885 Å² / B_iso min: 13.72 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	0 Å²	0.67 Å²
2-	-	-0.32 Å²	0 Å²
3-	-	-	0.1 Å²

Refinement step

Cycle: final / Resolution: 2.25→40.61 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	19075	0	798	1100	20973
B_iso mean	-	-	32.09	37.08	-
Num. residues	-	-	-	-	2510

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.015	20190
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	18508
X-RAY DIFFRACTION	r_angle_refined_deg	1.263	1.707	27386
X-RAY DIFFRACTION	r_angle_other_deg	0.897	1.687	43274
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.948	5	2482
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.607	23.811	942
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.774	15	3389
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.086	15	98
X-RAY DIFFRACTION	r_chiral_restr	0.061	0.2	2844
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	22508
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3400

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	5554	0.05
1	2	B	5554	0.05
2	1	A	5543	0.05
2	2	C	5543	0.05
3	1	A	5539	0.06
3	2	D	5539	0.06
4	1	A	5561	0.05
4	2	E	5561	0.05
5	1	A	5570	0.05
5	2	F	5570	0.05
6	1	A	5560	0.04
6	2	G	5560	0.04
7	1	A	5535	0.06
7	2	I	5535	0.06
8	1	A	5577	0.04
8	2	K	5577	0.04
9	1	A	5575	0.05
9	2	L	5575	0.05
10	1	A	5566	0.05
10	2	M	5566	0.05
11	1	A	5587	0.05
11	2	N	5587	0.05
12	1	A	5575	0.05
12	2	S	5575	0.05
13	1	A	5588	0.04
13	2	T	5588	0.04
14	1	B	5564	0.05
14	2	C	5564	0.05
15	1	B	5554	0.04
15	2	D	5554	0.04
16	1	B	5571	0.04
16	2	E	5571	0.04
17	1	B	5560	0.04
17	2	F	5560	0.04
18	1	B	5573	0.03
18	2	G	5573	0.03
19	1	B	5534	0.06
19	2	I	5534	0.06
20	1	B	5560	0.03
20	2	K	5560	0.03
21	1	B	5543	0.04
21	2	L	5543	0.04
22	1	B	5575	0.04
22	2	M	5575	0.04
23	1	B	5565	0.05
23	2	N	5565	0.05
24	1	B	5562	0.04
24	2	S	5562	0.04
25	1	B	5588	0.04
25	2	T	5588	0.04
26	1	C	5546	0.05
26	2	D	5546	0.05
27	1	C	5555	0.05
27	2	E	5555	0.05
28	1	C	5565	0.04
28	2	F	5565	0.04
29	1	C	5588	0.05
29	2	G	5588	0.05
30	1	C	5524	0.05
30	2	I	5524	0.05
31	1	C	5590	0.04
31	2	K	5590	0.04
32	1	C	5568	0.04
32	2	L	5568	0.04
33	1	C	5587	0.05
33	2	M	5587	0.05
34	1	C	5585	0.05
34	2	N	5585	0.05
35	1	C	5558	0.05
35	2	S	5558	0.05
36	1	C	5585	0.04
36	2	T	5585	0.04
37	1	D	5546	0.05
37	2	E	5546	0.05
38	1	D	5559	0.04
38	2	F	5559	0.04
39	1	D	5561	0.04
39	2	G	5561	0.04
40	1	D	5527	0.06
40	2	I	5527	0.06
41	1	D	5584	0.04
41	2	K	5584	0.04
42	1	D	5551	0.05
42	2	L	5551	0.05
43	1	D	5562	0.04
43	2	M	5562	0.04
44	1	D	5544	0.06
44	2	N	5544	0.06
45	1	D	5557	0.05
45	2	S	5557	0.05
46	1	D	5595	0.04
46	2	T	5595	0.04
47	1	E	5587	0.04
47	2	F	5587	0.04
48	1	E	5578	0.04
48	2	G	5578	0.04
49	1	E	5543	0.05
49	2	I	5543	0.05
50	1	E	5601	0.03
50	2	K	5601	0.03
51	1	E	5565	0.04
51	2	L	5565	0.04
52	1	E	5562	0.05
52	2	M	5562	0.05
53	1	E	5563	0.06
53	2	N	5563	0.06
54	1	E	5552	0.05
54	2	S	5552	0.05
55	1	E	5575	0.04
55	2	T	5575	0.04
56	1	F	5583	0.04
56	2	G	5583	0.04
57	1	F	5552	0.05
57	2	I	5552	0.05
58	1	F	5617	0.03
58	2	K	5617	0.03
59	1	F	5568	0.04
59	2	L	5568	0.04
60	1	F	5592	0.03
60	2	M	5592	0.03
61	1	F	5576	0.05
61	2	N	5576	0.05
62	1	F	5561	0.04
62	2	S	5561	0.04
63	1	F	5588	0.03
63	2	T	5588	0.03
64	1	G	5534	0.05
64	2	I	5534	0.05
65	1	G	5606	0.03
65	2	K	5606	0.03
66	1	G	5566	0.04
66	2	L	5566	0.04
67	1	G	5598	0.04
67	2	M	5598	0.04
68	1	G	5609	0.05
68	2	N	5609	0.05
69	1	G	5562	0.04
69	2	S	5562	0.04
70	1	G	5599	0.03
70	2	T	5599	0.03
71	1	I	5570	0.05
71	2	K	5570	0.05
72	1	I	5564	0.04
72	2	L	5564	0.04
73	1	I	5540	0.06
73	2	M	5540	0.06
74	1	I	5536	0.06
74	2	N	5536	0.06
75	1	I	5532	0.05
75	2	S	5532	0.05
76	1	I	5572	0.05
76	2	T	5572	0.05
77	1	K	5594	0.04
77	2	L	5594	0.04
78	1	K	5608	0.04
78	2	M	5608	0.04
79	1	K	5586	0.05
79	2	N	5586	0.05
80	1	K	5570	0.04
80	2	S	5570	0.04
81	1	K	5610	0.04
81	2	T	5610	0.04
82	1	L	5575	0.05
82	2	M	5575	0.05
83	1	L	5561	0.05
83	2	N	5561	0.05
84	1	L	5577	0.04
84	2	S	5577	0.04
85	1	L	5609	0.04
85	2	T	5609	0.04
86	1	M	5607	0.05
86	2	N	5607	0.05
87	1	M	5561	0.04
87	2	S	5561	0.04
88	1	M	5604	0.04
88	2	T	5604	0.04
89	1	N	5552	0.05
89	2	S	5552	0.05
90	1	N	5598	0.05
90	2	T	5598	0.05
91	1	S	5594	0.03
91	2	T	5594	0.03

LS refinement shell

Resolution: 2.243→2.301 Å / R_factor R_free error: 0 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.252	592	-
R_work	0.211	10608	-
all	-	11200	-
obs	-	-	91.36 %

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