PDB-5a0p: Apo-structure of metalloprotease Zmp1 from Clostridium difficile

ID or keywords:

Entry

Database: PDB / ID: 5a0p

Title

Apo-structure of metalloprotease Zmp1 from Clostridium difficile

Components

ZINC METALLOPROTEASE ZMP1

Keywords

HYDROLASE

Function / homology

Function and homology information

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

Biological species

CLOSTRIDIUM DIFFICILE (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.398 Å

Authors

Schacherl, M. / Pichlo, C. / Neundorf, I. / Baumann, U.

Citation

Journal: Structure / Year: 2015
Title: Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease Zmp1 Implicated in Motility of Clostridium Difficile.
Authors: Schacherl, M. / Pichlo, C. / Neundorf, I. / Baumann, U.

History

Deposition	Apr 22, 2015	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 5, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 16, 2015	Group: Database references
Revision 1.2	Jul 12, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Mar 6, 2019	Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0	Oct 23, 2019	Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1	May 8, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5a0p.cif.gz	238.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5a0p.ent.gz	198.8 KB	Display	PDB format
PDBx/mmJSON format	5a0p.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5a0p_validation.pdf.gz	422.4 KB	Display	wwPDB validaton report
Full document	5a0p_full_validation.pdf.gz	422.4 KB	Display
Data in XML	5a0p_validation.xml.gz	21.1 KB	Display
Data in CIF	5a0p_validation.cif.gz	32.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0p ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0p	HTTPS FTP

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Related structure data

Related structure data	5a0rC 5a0sC 5a0xC C: citing same article (ref.)
Similar structure data	6r52-1 6r53-1 5a0r-2 5n12-2 5a0s-1 6r55-1 6r56-2 6r51-2 6r4z-1 5z9q-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: ZINC METALLOPROTEASE ZMP1

B: ZINC METALLOPROTEASE ZMP1

hetero molecules

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

1

A: ZINC METALLOPROTEASE ZMP1

hetero molecules

defined by author&software
22 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ZINC METALLOPROTEASE ZMP1

hetero molecules

defined by author&software
22 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	43.169, 71.769, 117.798
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS oper: (Code: given
Matrix: (1, 0.0024, 0.0064), (-0.0022, 0.9991, -0.0415), (-0.0065, 0.0415, 0.9991)
Vector: -0.6713, -34.3469, -6.6411)

#1: Protein	ZINC METALLOPROTEASE ZMP1 / ZMP1 Mass: 21983.684 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: WITHOUT SIGNAL PEPTIDE (MISSING AA 1-26), CLEAVED N-TERMINAL HIS-TAG WITH THROMBIN, RESULTING GSH- OVERHANG Source: (gene. exp.) CLOSTRIDIUM DIFFICILE (bacteria) / Strain: 630 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR References: UniProt: Q183R7, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.28 Å³/Da / Density % sol: 46.11 % Description: SUBSTRUCTURE SOLVED BY ZINC-SAD USING PEAK DATA AT 1.28254 A, COLLECTED TO 1.67 A RESOLUTION
Crystal grow	Temperature: 293 K / pH: 8 Details: 2.1 M AMMONIUM PHOSPHATE, 0.1 M TRIS PH 8.0 AT 293 K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.4→45.5 Å / Num. obs: 71874 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / B_iso Wilson estimate: 13.29 Å² / R_merge(I) obs: 0.05 / Net I/σ(I): 15.66
Reflection shell	Resolution: 1.4→1.49 Å / Redundancy: 4.1 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 2.48 / % possible all: 95.6

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Processing

Software

Name	Version	Classification
PHENIX	(PHENIX.REFINE)	refinement
XDS		data reduction
XSCALE		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD
Starting model: NONE

Resolution: 1.398→45.53 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 17.21 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1817	3594	5 %
R_work	0.156	-	-
obs	0.1573	71852	98.21 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 17.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.398→45.53 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3062	0	2	532	3596

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3173
X-RAY DIFFRACTION	f_angle_d	1.022	4296
X-RAY DIFFRACTION	f_dihedral_angle_d	12.128	1168
X-RAY DIFFRACTION	f_chiral_restr	0.038	468
X-RAY DIFFRACTION	f_plane_restr	0.005	561

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 (%)
1.3985-1.4169	0.3207	124	0.2608	2357	X-RAY DIFFRACTION	90
1.4169-1.4363	0.2665	136	0.2343	2592	X-RAY DIFFRACTION	98
1.4363-1.4568	0.2107	135	0.2268	2566	X-RAY DIFFRACTION	98
1.4568-1.4786	0.2494	137	0.2125	2600	X-RAY DIFFRACTION	98
1.4786-1.5017	0.2168	136	0.1978	2584	X-RAY DIFFRACTION	98
1.5017-1.5263	0.2042	137	0.197	2604	X-RAY DIFFRACTION	98
1.5263-1.5526	0.2179	135	0.1914	2557	X-RAY DIFFRACTION	97
1.5526-1.5808	0.1792	135	0.1807	2559	X-RAY DIFFRACTION	98
1.5808-1.6112	0.2106	139	0.1726	2648	X-RAY DIFFRACTION	99
1.6112-1.6441	0.2047	139	0.1709	2626	X-RAY DIFFRACTION	99
1.6441-1.6799	0.2071	137	0.1697	2620	X-RAY DIFFRACTION	99
1.6799-1.719	0.1827	139	0.1637	2625	X-RAY DIFFRACTION	99
1.719-1.762	0.1764	138	0.154	2621	X-RAY DIFFRACTION	99
1.762-1.8096	0.1807	139	0.1546	2643	X-RAY DIFFRACTION	99
1.8096-1.8628	0.1616	138	0.147	2625	X-RAY DIFFRACTION	99
1.8628-1.923	0.1755	136	0.1525	2593	X-RAY DIFFRACTION	98
1.923-1.9917	0.1905	139	0.1511	2632	X-RAY DIFFRACTION	98
1.9917-2.0715	0.1629	136	0.1356	2594	X-RAY DIFFRACTION	98
2.0715-2.1657	0.1624	139	0.1396	2629	X-RAY DIFFRACTION	98
2.1657-2.2799	0.1659	140	0.1345	2665	X-RAY DIFFRACTION	99
2.2799-2.4227	0.1498	140	0.135	2655	X-RAY DIFFRACTION	99
2.4227-2.6098	0.1886	141	0.1422	2675	X-RAY DIFFRACTION	99
2.6098-2.8724	0.1801	142	0.1459	2703	X-RAY DIFFRACTION	99
2.8724-3.2879	0.162	142	0.15	2707	X-RAY DIFFRACTION	100
3.2879-4.142	0.155	142	0.1426	2696	X-RAY DIFFRACTION	98
4.142-45.5538	0.2112	153	0.1676	2882	X-RAY DIFFRACTION	99

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	5.5636	0.7206	-0.9855	9.3677	1.3769	3.4976	-0.1101	0.2542	0.5926	-0.3649	0.2462	-0.1213	-0.6536	0.0287	-0.077	0.218	0.0109	0.0198	0.174	0.0494	0.1717	39.4948	45.9385	2.3379
2	2.6139	-0.0644	-0.1581	1.5936	0.1714	2.2295	-0.1086	0.1413	-0.025	-0.054	0.0962	0.0618	-0.0776	-0.0914	-0.0067	0.0897	-0.0008	-0.0002	0.0982	0.0209	0.0507	36.5281	36.3077	4.1216
3	6.8655	-4.6022	-2.1939	3.2566	1.5171	5.1808	0.0663	0.4522	-0.0643	-0.4933	0.0378	0.3862	0.6184	-0.5045	-0.0278	0.2085	-0.0599	-0.0179	0.1702	0.0214	0.1893	30.2798	19.6462	7.0788
4	7.1092	0.8923	-0.2552	6.1779	1.9687	8.1102	-0.1406	-0.3414	-0.0937	0.1129	0.0583	-0.19	0.5206	0.1988	0.1286	0.2656	0.0017	0.0219	0.1594	0.0489	0.2316	35.8146	14.6357	19.839
5	1.5644	0.21	0.2041	1.2062	-0.2854	1.746	-0.0077	0.0405	-0.113	0.0285	0.0399	0.019	0.0371	-0.0491	-0.018	0.0824	0.0023	0.0011	0.085	-0.0017	0.0866	38.5505	28.5117	12.8952
6	2.1942	-0.3399	0.2817	1.9524	-0.7384	4.8318	-0.0315	0.132	-0.1682	-0.0012	-0.0075	-0.1964	0.1682	0.2312	0.0555	0.071	0.007	0.0202	0.1302	-0.0156	0.1656	58.3767	28.6072	13.6178
7	1.4526	-0.2017	-0.0356	1.7171	-0.7421	2.6311	-0.0587	-0.0267	-0.1521	0.0364	0.0287	-0.0407	0.1564	0.0571	0.0403	0.0957	-0.0029	0.0047	0.0675	-0.0145	0.0995	49.6556	29.7848	19.5773
8	3.4997	-0.7402	0.7881	2.5399	0.422	2.6647	-0.0196	-0.1915	0.226	0.1211	0.0714	-0.2254	-0.2163	0.2258	-0.0657	0.1038	-0.0326	-0.0102	0.0754	-0.0174	0.1279	53.1885	41.1521	17.6372
9	5.1659	-0.7133	-1.1239	1.7104	0.264	5.4591	0.0189	0.1902	0.597	-0.1515	0.1818	-0.0672	-0.7861	0.0072	-0.1208	0.2238	0.0234	0.0398	0.1587	0.0764	0.2429	40.8184	81.6826	5.1915
10	2.576	0.3215	0.1128	1.8113	0.3311	2.3348	-0.0344	0.0957	-0.0058	-0.0037	0.0246	0.0529	-0.0471	-0.3006	0.0125	0.0972	0.0158	0.0084	0.1195	0.0248	0.0826	31.0657	72.7393	11.1515
11	2.3345	-0.0545	-1.9939	0.3828	-0.518	2.5224	-0.1547	0.3817	-0.0674	-0.0997	0.1311	-0.0415	-0.0018	-0.0354	0.0252	0.0914	-0.001	0.0018	0.1357	0.0109	0.067	43.1674	69.4396	4.8801
12	8.0152	-5.5381	-0.3691	3.9322	0.6125	1.8257	0.2669	0.0496	-0.1883	-0.4589	-0.0278	0.4448	0.1183	-0.3528	-0.1775	0.1809	-0.0392	-0.0127	0.1521	-0.0008	0.1916	31.1497	54.5428	11.6303
13	1.3304	0.7946	-0.2129	3.4391	-0.2182	5.4766	0.0051	-0.1423	0.0479	-0.0299	0.0428	0.1027	-0.1666	-0.0006	-0.0301	0.1756	0.0006	0.0141	0.1139	-0.0143	0.2099	37.8445	51.1528	24.1056
14	1.5298	0.1002	-0.0972	0.644	-0.4052	1.4559	-0.0245	0.0819	-0.1308	-0.0117	-0.0209	0.0394	0.0442	-0.0377	0.0451	0.095	0.0045	-0.0009	0.0796	-0.0091	0.0929	38.8085	63.9535	17.3527
15	2.1084	-0.1239	0.4044	1.8336	0.0087	4.1587	0.0006	0.0787	-0.1058	-0.0106	-0.0408	-0.1697	0.1395	0.2384	-0.0231	0.0968	0.012	0.0136	0.1463	0.0051	0.1385	58.6911	63.6211	18.0346
16	1.1948	0.1785	-0.1754	1.5667	-0.1539	2.2924	-0.011	-0.0297	-0.0559	0.0629	-0.0103	-0.0373	0.0767	0.1201	0.0194	0.0945	0.0021	0.0011	0.0714	-0.0068	0.0887	49.873	65.251	23.8693
17	5.4245	-1.7939	1.8366	2.2295	0.6314	2.6953	-0.1993	-0.4491	0.487	0.184	0.1266	-0.0091	-0.2252	-0.1101	-0.0312	0.1521	-0.0098	-0.0099	0.0758	-0.0138	0.1331	48.7961	78.4693	25.4684
18	3.0626	-0.8683	1.5516	3.0846	-0.2057	2.0193	-0.0876	0.1384	0.2902	0.0145	-0.1414	-0.4816	-0.3891	0.3764	0.2267	0.1166	-0.0339	-0.0027	0.1303	0.01	0.1631	57.72	74.8915	18.2293

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 26 THROUGH 40 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 41 THROUGH 82 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 83 THROUGH 95 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 96 THROUGH 109 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 110 THROUGH 151 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 152 THROUGH 169 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 170 THROUGH 195 )
8	X-RAY DIFFRACTION	8	CHAIN 'A' AND (RESID 196 THROUGH 220 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 26 THROUGH 40 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 41 THROUGH 63 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 64 THROUGH 82 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 83 THROUGH 95 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 96 THROUGH 109 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 110 THROUGH 151 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 152 THROUGH 169 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 170 THROUGH 195 )
17	X-RAY DIFFRACTION	17	CHAIN 'B' AND (RESID 196 THROUGH 207 )
18	X-RAY DIFFRACTION	18	CHAIN 'B' AND (RESID 208 THROUGH 220 )

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