PDB-6r4y: Crystal structure of holo PPEP-1(E143A/Y178F) in complex with pro...

ID or keywords:

Entry

Database: PDB / ID: 6r4y

Title

Crystal structure of holo PPEP-1(E143A/Y178F) in complex with product peptide Ac-EVNP-CO2 (substrate peptide: Ac-EVNPAVP-CONH2)

Components

ACE-GLU-VAL-ASN-PRO
Pro-Pro endopeptidase

Keywords

HYDROLASE / Pro-Pro endopeptidase 1 / zinc metallopeptidase / Clostridium difficile / virulence factor

Function / homology

Function and homology information

Pro-Pro endopeptidase / metallopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function

Biological species

Peptoclostridium difficile (bacteria)

Clostridioides difficile (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.452 Å

Authors

Pichlo, C. / Baumann, U.

Citation

Journal: J.Biol.Chem. / Year: 2019
Title: Molecular determinants of the mechanism and substrate specificity ofClostridium difficileproline-proline endopeptidase-1.
Authors: Pichlo, C. / Juetten, L. / Wojtalla, F. / Schacherl, M. / Diaz, D. / Baumann, U.

History

Deposition	Mar 24, 2019	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 12, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jun 26, 2019	Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Aug 7, 2019	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3	Jan 24, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4	Oct 23, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6r4y.cif.gz	243.1 KB	Display	PDBx/mmCIF format
PDB format	pdb6r4y.ent.gz	198.7 KB	Display	PDB format
PDBx/mmJSON format	6r4y.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r4/6r4y ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r4y	HTTPS FTP

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Related structure data

Related structure data	6r4wC 6r4xC 6r4zC 6r50C 6r51C 6r52C 6r53C 6r54C 6r55C 6r56C 6r57C 6r58C 6r59C 6r5aC 6r5bC 6r5cC 6r9zC 5a0pS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6r57-1 6r5a-2 6r59-1 6r58-2 5a0r-1 5no9-3 5a0x-2 6r51-1 6svw-d 2l28-d 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
Related items in Molecule of the Month	#28 - Apr 2002 Anthrax Toxin similarity (3) #44 - Aug 2003 Calmodulin similarity (3) #237 - Sep 2019 Nanodiscs and HDL similarity (1)

Deposited unit

A: Pro-Pro endopeptidase

B: Pro-Pro endopeptidase

D: ACE-GLU-VAL-ASN-PRO

E: ACE-GLU-VAL-ASN-PRO

hetero molecules

44.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Pro-Pro endopeptidase

E: ACE-GLU-VAL-ASN-PRO

hetero molecules

defined by author&software
Evidence: The peptide is proteolytically cleaved by PPEP-1 implying that the peptide has to form a complex with the protease
22.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pro-Pro endopeptidase

D: ACE-GLU-VAL-ASN-PRO

hetero molecules

defined by author&software
22.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	37.036, 42.800, 118.274
Angle α, β, γ (deg.)	90.00, 92.78, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pro-Pro endopeptidase / PPEP-1 / Zinc metalloprotease Zmp1 Mass: 21909.646 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Peptoclostridium difficile (bacteria) / Gene: zmp1, ppep-1, CD630_28300 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Star / References: UniProt: Q183R7, Pro-Pro endopeptidase
#2: Protein/peptide	ACE-GLU-VAL-ASN-PRO Mass: 483.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Clostridioides difficile (bacteria)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 376 / Source method: isolated from a natural source / Formula: H₂O
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: 2.09 Å³/Da / Density % sol: 41.17 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop Details: 1.5 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide (Ac-EVNPAVP-CONH2) in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 1.5 microl precipitant solution ...Details: 1.5 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide (Ac-EVNPAVP-CONH2) in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 8.5, 2.1 M ammonium phosphate dibasic. Reservoir volume: 200 microl

Crystal

Density Matthews: 2.09 Å³/Da / Density % sol: 41.17 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.5 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide (Ac-EVNPAVP-CONH2) in 20 mM Tris pH 7.5, 200 mM NaCl, 0.1 mM ZnCl2 was mixed with 1.5 microl precipitant solution ...

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 16, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.452→40.24 Å / Num. obs: 64508 / % possible obs: 98.18 % / Redundancy: 5.6 % / Net I/σ(I): 16.62
Reflection shell	Resolution: 1.452→1.504 Å

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Processing

Software

Name	Version	Classification
PHENIX	(1.15rc1_3420: ???)	refinement
XDS	20160617	data reduction
XDS	20160617	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p

Resolution: 1.452→40.24 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 16.53

	R_factor	Num. reflection	% reflection
R_free	0.1652	2001	3.1 %
R_work	0.1451	-	-
obs	0.1457	64508	98.15 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 1.452→40.24 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3083	0	2	376	3461

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3225
X-RAY DIFFRACTION	f_angle_d	0.896	4379
X-RAY DIFFRACTION	f_dihedral_angle_d	13.109	1189
X-RAY DIFFRACTION	f_chiral_restr	0.071	479
X-RAY DIFFRACTION	f_plane_restr	0.007	578

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 (%)
1.4516-1.4879	0.2372	140	0.2438	4278	X-RAY DIFFRACTION	95
1.4879-1.5281	0.2312	136	0.2111	4364	X-RAY DIFFRACTION	96
1.5281-1.5731	0.205	135	0.194	4338	X-RAY DIFFRACTION	97
1.5731-1.6239	0.2363	136	0.1741	4399	X-RAY DIFFRACTION	97
1.6239-1.6819	0.1959	140	0.1638	4439	X-RAY DIFFRACTION	98
1.6819-1.7493	0.1867	151	0.1591	4426	X-RAY DIFFRACTION	98
1.7493-1.8289	0.1728	143	0.1518	4467	X-RAY DIFFRACTION	98
1.8289-1.9253	0.1742	143	0.1465	4447	X-RAY DIFFRACTION	99
1.9253-2.0459	0.1592	138	0.1408	4505	X-RAY DIFFRACTION	99
2.0459-2.2039	0.1528	141	0.1323	4511	X-RAY DIFFRACTION	99
2.2039-2.4256	0.1471	153	0.1289	4514	X-RAY DIFFRACTION	99
2.4256-2.7766	0.145	150	0.135	4531	X-RAY DIFFRACTION	99
2.7766-3.4979	0.1708	147	0.1426	4594	X-RAY DIFFRACTION	100
3.4979-40.2559	0.1481	148	0.1336	4694	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	0.1817	0.0411	-0.0266	0.2597	0.1872	0.3332	0.1083	0.6164	0.19	-0.5163	0.0077	-0.3576	-0.0486	0.2637	-0.0004	0.2797	0.0083	0.0757	0.2849	-0.0284	0.2036	9.2248	25.6946	-0.935
2	0.1375	0.2743	-0.0254	0.5668	-0.1677	0.6751	-0.0012	0.0977	0.0313	-0.2022	-0.0743	0.0336	-0.2032	0.0681	-0	0.2193	-0.0116	0.0127	0.147	0.0016	0.1835	3.7225	34.5134	8.2172
3	0.3653	0.3749	0.1019	0.4623	-0.1176	0.6637	0.0801	0.1314	-0.0797	-0.2621	-0.1045	-0.0219	0.0212	-0.054	0	0.2164	0.0044	0.0097	0.177	-0.0208	0.154	-0.6946	21.6564	3.5243
4	0.3311	0.0902	-0.2507	0.1891	0.0512	0.2761	-0.0393	0.0983	0.5193	-0.0981	0.2133	0.2411	-0.2782	-0.3933	0.0009	0.1734	0.0138	0.0013	0.2099	0.0324	0.2552	-12.7652	32.3344	15.623
5	2.8195	-0.9272	0.9983	0.6593	-0.9259	1.3622	-0.428	-0.941	0.2269	0.4856	0.4318	-0.0616	-0.2212	-0.1233	-0.4805	0.2158	0.125	0.0373	0.3895	0.0097	0.1672	-10.5645	25.266	27.808
6	1.1201	-0.2872	0.0373	1.4513	-0.3501	1.4029	-0.0139	-0.0762	0.0456	0.0637	-0.0105	-0.1185	-0.0906	-0.053	0	0.135	-0.0022	-0.0066	0.1398	0.0054	0.1332	-1.0235	25.6894	17.3695
7	0.5004	0.0088	-0.4509	0.4307	0.076	0.4831	0.0864	-0.1481	-0.0546	-0.0162	-0.0501	0.0044	0.5023	-0.2307	0.0001	0.2605	-0.0134	-0.0213	0.142	-0.0047	0.1656	0.2484	6.1077	17.8141
8	0.8777	-0.4033	0.6553	0.9538	-0.2084	0.5686	-0.0102	-0.1263	0.0046	0.189	0.0374	-0.17	0.0588	-0.0678	0.0001	0.1589	0.0005	-0.0289	0.1639	0.0115	0.1681	3.4954	15.0218	22.5714
9	0.0357	0.1624	0.0013	0.7747	-0.0908	0.2363	0.1622	0.0326	-0.0764	0.1856	-0.1549	-0.384	0.0629	0.3618	-0.0389	0.1217	0.009	-0.0299	0.1994	0.0283	0.2427	15.8613	16.5373	19.6151
10	0.5306	-0.0308	-0.0144	0.4251	-0.0462	0.2242	-0.0146	0.1501	-0.2354	-0.2322	-0.0403	-0.182	0.4712	0.2591	-0.0003	0.22	0.0384	0.0103	0.1711	-0.0188	0.2315	10.3368	7.3208	12.9051
11	1.1318	-0.6733	-0.2775	0.917	-0.0472	1.4535	0.0111	-0.0496	0.0078	0.0044	-0.0984	-0.1406	-0.0024	0.032	-0	0.1154	0.0019	-0.0028	0.1533	0.0073	0.1631	18.8616	11.679	52.1654
12	0.4689	-0.3884	0.3218	0.6575	0.1615	0.7636	0.0712	-0.0859	-0.0013	0.0762	-0.1107	-0.0509	-0.0563	-0.004	0	0.1367	-0.0111	-0.0086	0.1556	-0.0097	0.1434	13.4227	20.8352	56.7172
13	0.4256	-0.2491	-0.033	0.2005	0.1787	0.4626	0.0593	-0.3144	-0.4545	0.2358	0.1172	0.0725	0.4265	-0.1263	0.0138	0.1537	-0.0043	-0.0305	0.1676	0.0325	0.2193	-1.5604	8.4775	51.7436
14	0.38	-0.2557	0.0806	0.4316	0.27	0.4223	0.1366	0.4415	-0.0743	-0.289	-0.1103	0.109	-0.3205	-0.083	-0.0128	0.2655	0.0305	-0.0198	0.3382	0.0123	0.2702	-6.5822	15.1977	40.3188
15	1.2139	-0.1111	0.3656	1.5464	-0.1448	0.8501	0.0466	0.0377	-0.0366	-0.0872	-0.0378	0.0256	-0.0055	-0.0066	0	0.1369	0.0097	-0.0111	0.136	-0.0009	0.1246	6.8161	16.7785	44.9448
16	0.6238	-0.0483	0.3389	0.7239	0.2978	0.3297	0.0256	0.0217	0.1388	0.1001	-0.0058	0.0539	-0.2682	-0.097	-0.0001	0.231	0.0076	0.014	0.1556	0.0015	0.1888	5.2078	36.8159	45.3201
17	0.5567	0.1132	-0.5888	1.2489	-0.1376	0.734	-0.0047	0.1238	0.1238	-0.3404	0.0337	0.0329	-0.1181	-0.0925	-0	0.1902	0.0121	0.0146	0.1746	0.0201	0.1542	6.7894	28.0314	38.9661
18	1.5752	0.7369	0.9168	0.6412	0.2082	0.6993	0.023	0.2935	-0.0355	-0.2677	0.1047	-0.3242	-0.3524	0.4115	0.4189	0.2244	-0.0235	0.1026	0.1985	0.002	0.1756	18.9211	28.9649	35.6005
19	0.3351	0.0567	-0.3133	0.3194	-0.1598	0.3299	-0.0059	0.0352	0.2387	-0.0841	-0.0357	-0.5697	-0.2267	0.4031	0.0265	0.2388	-0.0136	0.0192	0.1651	0.0109	0.2332	16.3416	36.706	44.1156
20	0.0933	-0.0427	-0.088	0.0232	0.0406	0.0875	0.1389	-0.4618	0.2711	0.4442	0.137	0.2006	-0.5338	-0.3245	0.0025	0.2808	0.0123	-0.0007	0.2551	-0.0321	0.2619	-0.3071	21.4326	48.2823
21	0.0157	0.0179	-0.0149	0.0512	0.0042	0.043	0.2782	-0.0787	-0.4898	-0.1188	0.1098	0.0463	0.4039	-0.2902	-0.001	0.1958	-0.0278	-0.0278	0.2166	0.0053	0.201	-7.9627	19.747	17.7183

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 40 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 41 through 63 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 64 through 82 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 83 through 95 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 96 through 109 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 110 through 151 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 152 through 169 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 170 through 195 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 196 through 208 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 209 through 220 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 29 through 63 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 64 through 82 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 83 through 95 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 96 through 109 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 110 through 151 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 152 through 169 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 170 through 195 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 196 through 208 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 209 through 220 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 1 through 4 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1 through 4 )

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