PDB-6r59: Crystal structure of PPEP-1(E143A/Y178F) in complex with substrat...

ID or keywords:

Entry

Database: PDB / ID: 6r59

Title

Crystal structure of PPEP-1(E143A/Y178F) in complex with substrate peptide Ac-EVAPPVP-NH2

Components

ACE-GLU-VAL-ALA-PRO-PRO-VAL-LPD
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: 1.65 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 / diffrn_source Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _diffrn_source.pdbx_synchrotron_site
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.pdbx_ptnr1_label_alt_id / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6r59.cif.gz	249.9 KB	Display	PDBx/mmCIF format
PDB format	pdb6r59.ent.gz	205.3 KB	Display	PDB format
PDBx/mmJSON format	6r59.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r5/6r59 ftp://data.pdbj.org/pub/pdb/validation_reports/r5/6r59	HTTPS FTP

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Related structure data

Related structure data	6r4wC 6r4xC 6r4yC 6r4zC 6r50C 6r51C 6r52C 6r53C 6r54C 6r55C 6r56C 6r57C 6r58C 6r5aC 6r5bC 6r5cC 6r9zC 5a0pS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6r51-1 5a0r-1 6r57-1 6r58-2 6r5b-1 6r58-4 5a0x-2 6r57-2 6r5a-2 6r5c-2 6r4y-1 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

E: ACE-GLU-VAL-ALA-PRO-PRO-VAL-LPD

C: ACE-GLU-VAL-ALA-PRO-PRO-VAL-LPD

hetero molecules

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

1

A: Pro-Pro endopeptidase

E: ACE-GLU-VAL-ALA-PRO-PRO-VAL-LPD

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
22.6 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Pro-Pro endopeptidase

C: ACE-GLU-VAL-ALA-PRO-PRO-VAL-LPD

hetero molecules

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

Unit cell

Length a, b, c (Å)	37.110, 42.950, 122.240
Angle α, β, γ (deg.)	90.00, 96.60, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Pro-Pro endopeptidase / PPEP-1 / Zinc metalloprotease Zmp1 Mass: 21822.568 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-ALA-PRO-PRO-VAL-LPD Mass: 732.867 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 / Water Mass: 18.015 Da / Num. of mol.: 268 / 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: 2.15 Å³/Da / Density % sol: 42.66 %
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 in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 9.0, 2.1 M ...Details: 1.5 microl 12 mg per ml rPPEP-1 E143A Y178F with 6 mM substrate peptide in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 9.0, 2.1 M ammonium phosphate dibasic. Reservoir volume: 200 microl

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.66 %

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 in 20 mM Tris pH 7.5, 200 mM NaCl was mixed with 1.5 microl precipitant solution containing: 100 mM Tris pH 9.0, 2.1 M ...

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Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2016
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.65→40.492 Å / Num. obs: 44656 / % possible obs: 96 % / Redundancy: 2.6 % / Net I/σ(I): 12.7
Reflection shell	Resolution: 1.65→1.71 Å

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Processing

Software

Name	Version	Classification
PHENIX	(dev_3395: ???)	refinement
XDS	20160617	data reduction
XDS	20160617	data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5A0P

5a0p

Resolution: 1.65→40.492 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.16

	R_factor	Num. reflection	% reflection
R_free	0.2195	1923	4.31 %
R_work	0.1914	-	-
obs	0.1926	44656	96.19 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.65→40.492 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3119	0	2	268	3389

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	3308
X-RAY DIFFRACTION	f_angle_d	0.734	4499
X-RAY DIFFRACTION	f_dihedral_angle_d	9.173	1985
X-RAY DIFFRACTION	f_chiral_restr	0.048	490
X-RAY DIFFRACTION	f_plane_restr	0.005	595

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 (%)
1.65-1.6913	0.3806	131	0.3284	3018	X-RAY DIFFRACTION	95
1.6913-1.737	0.3225	138	0.3056	2962	X-RAY DIFFRACTION	95
1.737-1.7881	0.3913	140	0.2872	3033	X-RAY DIFFRACTION	96
1.7881-1.8458	0.279	132	0.2715	2961	X-RAY DIFFRACTION	94
1.8458-1.9118	0.2737	142	0.2579	3013	X-RAY DIFFRACTION	96
1.9118-1.9883	0.2758	145	0.2495	3023	X-RAY DIFFRACTION	96
1.9883-2.0788	0.2692	134	0.2395	3066	X-RAY DIFFRACTION	96
2.0788-2.1884	0.2299	128	0.2217	3081	X-RAY DIFFRACTION	96
2.1884-2.3255	0.2627	135	0.2038	3029	X-RAY DIFFRACTION	96
2.3255-2.505	0.2186	139	0.1951	3084	X-RAY DIFFRACTION	97
2.505-2.7571	0.2735	137	0.2027	3076	X-RAY DIFFRACTION	97
2.7571-3.1559	0.2239	137	0.1889	3074	X-RAY DIFFRACTION	96
3.1559-3.9756	0.1731	139	0.1568	3103	X-RAY DIFFRACTION	97
3.9756-40.5039	0.1604	146	0.1454	3210	X-RAY DIFFRACTION	97

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	2.5205	1.1314	0.01	5.0736	-1.3102	4.009	0.1073	-0.1783	0.1121	0.7147	-0.0311	0.3461	-0.3277	-0.2454	-0.1166	0.3919	0.0355	0.1056	0.2124	-0.0105	0.2307	6.7088	20.2836	55.8138
2	2.3975	0.8598	-0.2693	3.4476	-0.2608	2.3296	0.1169	0.0407	-0.0177	-0.0567	-0.1163	-0.1386	0.0881	0.1263	-0.007	0.2681	0.0386	0.0135	0.1656	0.0151	0.202	16.2731	14.6139	45.0623
3	4.7656	0.0545	2.4471	5.4211	0.5655	2.0453	0.1105	0.1242	-0.2733	-0.1793	-0.1677	-0.1833	0.6732	0.1144	-0.2303	0.5071	0.0491	0.0238	0.2337	0.0349	0.2906	11.9116	-5.1622	42.8825
4	3.6718	0.0853	-0.7969	4.7101	0.1477	2.7787	-0.089	0.154	-0.1589	-0.2326	0.0559	0.366	0.4531	-0.1814	-0.0377	0.3527	-0.0228	-0.0674	0.2032	0.0019	0.2886	4.0439	2.3637	40.814
5	1.4952	-0.332	2.0351	3.317	-0.4885	2.7775	0.108	0.7385	-0.4911	-0.2116	0.1804	-0.5677	0.043	-0.1148	-0.1213	0.2245	0.0853	-0.0113	0.6136	-0.2266	0.37	7.3071	9.2321	2.5668
6	3.6512	-0.1744	0.8484	5.3647	-0.1156	4.2613	0.228	0.5516	0.0965	0.035	-0.0225	0.0025	-0.3073	-0.0733	-0.1766	0.129	0.0416	0.0271	0.3486	0.0305	0.1656	0.5827	19.7686	9.6112
7	1.0985	0.4373	-0.1883	0.6807	0.4322	0.5382	0.2391	0.6396	-0.3474	0.0375	0.1578	-0.1312	0.1425	0.0468	1.1088	0.0468	0.1003	-0.11	0.6829	-0.2585	0.3359	-2.2778	6.4476	2.6209
8	1.707	0.8818	1.3237	1.3521	0.6208	1.8881	0.1636	0.8762	0.3343	-0.3494	-0.0213	0.3166	-0.3819	-0.3464	0.0415	0.2142	0.0942	0.0307	0.4025	0.0013	0.3109	-17.3061	19.0236	7.2789
9	8.7839	-2.7131	1.837	5.8127	1.0189	8.6971	-0.0337	-0.1634	-0.4741	0.6272	-0.1295	0.6014	-0.0673	-0.631	0.2061	0.2163	-0.0438	0.06	0.2972	-0.0484	0.2533	-22.1102	12.3583	18.9416
10	2.4069	1.6976	0.5924	1.2905	-0.131	3.5468	0.1195	0.7332	-0.1711	-0.0929	-0.1516	0.2052	-0.1501	-0.2759	0.0924	0.1212	0.0398	-0.0272	0.3631	-0.0785	0.2149	-13.6271	13.5283	11.2916
11	4.5322	-1.2118	-0.9304	6.5411	-1.8996	5.1217	0.2437	-0.1365	-0.0499	0.8792	-0.155	-0.0504	0.0265	0.2321	-0.0349	0.3217	-0.0437	-0.0407	0.2372	-0.0361	0.2166	-5.9689	14.4083	20.8984
12	0.8278	0.4657	0.0844	1.064	0.7597	0.6633	-0.0103	0.4852	-1.0318	0.4781	-0.1318	0.0194	0.5661	-0.3652	0.0806	0.3712	-0.041	0.0035	0.3306	-0.2644	0.6217	-8.8046	-2.854	13.0856
13	6.6261	1.4051	0.4185	3.6431	-0.7852	2.348	0.1966	-0.4648	-0.7155	1.1176	-0.4854	0.5769	0.5781	-0.2889	-0.1349	0.68	-0.1289	0.1185	0.2757	-0.0647	0.6004	-13.49	-0.4555	25.2448
14	3.1826	1.3214	-0.7069	3.9295	0.8647	2.739	0.1079	0.1776	-0.7479	0.686	-0.1673	0.2139	0.2845	-0.0695	-0.0507	0.4077	0.007	-0.0584	0.2174	-0.1116	0.5147	-5.0998	0.108	17.2651
15	1.0064	0.5162	0.1326	2.8314	-3.2162	4.2283	0.2443	-0.1204	-0.4884	1.095	-0.1835	-0.352	0.4044	0.3344	-0.0803	0.5963	0.0155	-0.1954	0.2362	-0.0229	0.4888	3.9651	0.6888	24.0064
16	2.238	-0.152	0.504	2.6196	0.9338	4.6157	0.0955	0.3158	-0.9991	0.4396	-0.1838	-0.2745	0.786	0.2329	-0.0393	0.6552	0.06	-0.1375	0.2979	-0.1595	0.842	0.9414	-8.3554	16.3437
17	0.0487	-0.014	0.0451	0.0243	-0.0205	0.041	0.179	-0.1121	0.1867	-0.2478	-0.0016	0.2096	-0.1762	0.1308	-0.0005	0.4058	0.0579	0.0202	0.3664	0.034	0.2454	18.2081	10.0417	41.079
18	0.0957	0.0452	-0.0428	0.1419	-0.1274	0.1828	0.1766	-0.0107	-0.017	0.3852	0.1657	0.1093	-0.0288	0.0235	0.2226	0.2302	-0	-0.0151	0.3212	-0.0855	0.2512	-15.0526	7.0622	13.7068

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 63 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 64 through 151 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 152 through 169 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 170 through 220 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 29 through 41 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 42 through 63 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 64 through 82 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 83 through 95 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 96 through 109 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 110 through 124 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 125 through 138 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 139 through 169 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 170 through 182 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 183 through 195 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 196 through 207 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 208 through 220 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 119 through 124 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 119 through 124 )

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