PDB-5a0r: Product peptide-bound structure of metalloprotease Zmp1 variant E...

ID or keywords:

Entry

Database: PDB / ID: 5a0r

Title

Product peptide-bound structure of metalloprotease Zmp1 variant E143A from Clostridium difficile

Components

PRODUCT PEPTIDE
ZINC METALLOPROTEASE ZMP1

Keywords

HYDROLASE / METALLOPROTEASE / ZMP1 / PROLINE SPECIFICITY

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)
SYNTHETIC CONSTRUCT (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.251 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	Mar 6, 2019	Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
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	Jan 10, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_asym_id / _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_asym_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2	Nov 13, 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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Download

PDBx/mmCIF format	5a0r.cif.gz	244.5 KB	Display	PDBx/mmCIF format
PDB format	pdb5a0r.ent.gz	202.7 KB	Display	PDB format
PDBx/mmJSON format	5a0r.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5a0r_validation.pdf.gz	439.9 KB	Display	wwPDB validaton report
Full document	5a0r_full_validation.pdf.gz	440.3 KB	Display
Data in XML	5a0r_validation.xml.gz	20.8 KB	Display
Data in CIF	5a0r_validation.cif.gz	31.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/a0/5a0r ftp://data.pdbj.org/pub/pdb/validation_reports/a0/5a0r	HTTPS FTP

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Related structure data

Related structure data	5a0pSC 5a0sC 5a0xC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6r59-1 6r59-2 6r51-1 6r58-2 6r5b-1 6r5c-2 5a0x-2 6r57-1 6dp0-d 3rxl-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: ZINC METALLOPROTEASE ZMP1

B: ZINC METALLOPROTEASE ZMP1

D: PRODUCT PEPTIDE

E: PRODUCT PEPTIDE

hetero molecules

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

1

A: ZINC METALLOPROTEASE ZMP1

D: PRODUCT PEPTIDE

hetero molecules

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

2

B: ZINC METALLOPROTEASE ZMP1

E: PRODUCT PEPTIDE

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)	37.060, 42.960, 119.210
Angle α, β, γ (deg.)	90.00, 92.54, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2

/ NCS ensembles :

ID
1
2

NCS oper: (Code: given
Matrix: (0.864, 0.1518, -0.4801), (0.1323, -0.9884, -0.0744), (-0.4858, 0.0008, -0.8741)
Vector: 124.5911, 9.1758, 483.6919)

#1: Protein	ZINC METALLOPROTEASE ZMP1 / ZMP1 Mass: 21925.646 Da / Num. of mol.: 2 / Mutation: YES 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: Protein/peptide	PRODUCT PEPTIDE Mass: 483.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 454 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y
Nonpolymer details	ACETYLATION (ACE): ACETYLATION AT THE N-TERMINUS OF PRODUCT PEPTIDE GLYCEROL (GOL): ORIGINATES FROM ...ACETYLATION (ACE): ACETYLATION AT THE N-TERMINUS OF PRODUCT PEPTIDE GLYCEROL (GOL): ORIGINATES FROM CRYO-SOLUTION

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.14 % / Description: NONE
Crystal grow	Temperature: 293 K / pH: 7 Details: 1.8 M AMMONIUM PHOSPHATE DIBASIC, 0.1 M TRIS PH 8.5 GROWN 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 2M / Detector: PIXEL / Date: Oct 9, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.25→40.4 Å / Num. obs: 102218 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 4 % / B_iso Wilson estimate: 12.32 Å² / R_merge(I) obs: 0.04 / Net I/σ(I): 15.82
Reflection shell	Resolution: 1.25→1.33 Å / Redundancy: 3.6 % / R_merge(I) obs: 0.45 / Mean I/σ(I) obs: 2.67 / % possible all: 93.7

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5A0P

5a0p

Resolution: 1.251→40.411 Å / SU ML: 0.1 / σ(F): 1.36 / Phase error: 15.3 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.162	5111	5 %
R_work	0.1415	-	-
obs	0.1425	102215	98.55 %

Solvent computation

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

Displacement parameters

B_iso mean: 19.02 Å²

Refinement step

Cycle: LAST / Resolution: 1.251→40.411 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3080	0	26	454	3560

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.015	3237
X-RAY DIFFRACTION	f_angle_d	1.489	4387
X-RAY DIFFRACTION	f_dihedral_angle_d	12.825	1191
X-RAY DIFFRACTION	f_chiral_restr	0.069	476
X-RAY DIFFRACTION	f_plane_restr	0.009	574

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 (%)
1.2508-1.265	0.2657	143	0.2428	2726	X-RAY DIFFRACTION	81
1.265-1.2799	0.2375	165	0.2179	3127	X-RAY DIFFRACTION	97
1.2799-1.2955	0.2111	164	0.2185	3131	X-RAY DIFFRACTION	96
1.2955-1.3119	0.2201	166	0.2047	3147	X-RAY DIFFRACTION	97
1.3119-1.3292	0.215	168	0.2021	3197	X-RAY DIFFRACTION	98
1.3292-1.3474	0.1868	169	0.1886	3203	X-RAY DIFFRACTION	98
1.3474-1.3667	0.2206	170	0.1884	3229	X-RAY DIFFRACTION	100
1.3667-1.3871	0.2009	173	0.1845	3292	X-RAY DIFFRACTION	99
1.3871-1.4087	0.1949	168	0.1802	3194	X-RAY DIFFRACTION	100
1.4087-1.4318	0.2127	176	0.1711	3340	X-RAY DIFFRACTION	100
1.4318-1.4565	0.1707	169	0.1671	3217	X-RAY DIFFRACTION	100
1.4565-1.483	0.1754	174	0.1614	3289	X-RAY DIFFRACTION	100
1.483-1.5115	0.1598	168	0.1545	3200	X-RAY DIFFRACTION	100
1.5115-1.5424	0.1644	175	0.146	3317	X-RAY DIFFRACTION	100
1.5424-1.5759	0.1694	169	0.1451	3230	X-RAY DIFFRACTION	100
1.5759-1.6126	0.166	174	0.1416	3302	X-RAY DIFFRACTION	100
1.6126-1.6529	0.1556	171	0.1433	3238	X-RAY DIFFRACTION	100
1.6529-1.6976	0.159	171	0.1466	3248	X-RAY DIFFRACTION	100
1.6976-1.7476	0.165	171	0.1482	3255	X-RAY DIFFRACTION	100
1.7476-1.804	0.1825	171	0.1418	3250	X-RAY DIFFRACTION	99
1.804-1.8684	0.164	173	0.141	3292	X-RAY DIFFRACTION	99
1.8684-1.9432	0.1515	172	0.1381	3258	X-RAY DIFFRACTION	99
1.9432-2.0317	0.1539	172	0.1327	3264	X-RAY DIFFRACTION	99
2.0317-2.1388	0.1252	171	0.1267	3255	X-RAY DIFFRACTION	99
2.1388-2.2728	0.13	173	0.1244	3282	X-RAY DIFFRACTION	99
2.2728-2.4482	0.1374	173	0.1252	3286	X-RAY DIFFRACTION	100
2.4482-2.6946	0.1622	174	0.1314	3313	X-RAY DIFFRACTION	100
2.6946-3.0844	0.1647	174	0.1352	3307	X-RAY DIFFRACTION	100
3.0844-3.8855	0.1577	173	0.126	3291	X-RAY DIFFRACTION	99
3.8855-40.4322	0.1583	181	0.1326	3424	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	0.909	0.43	0.273	3.2948	1.0164	1.5215	-0.0402	0.0965	-0.0269	-0.244	0.0196	-0.09	-0.0536	0.0508	0.0211	0.1176	-0.0089	0.022	0.0706	0.0082	0.0633	-44.064	-1.8462	242.7659
2	7.7592	4.5164	-2.4986	2.6752	-1.2194	2.7351	-0.0278	0.1041	0.4427	-0.0543	0.1581	0.3292	-0.2427	-0.252	-0.0998	0.1161	0.0326	-0.0052	0.1374	0.0095	0.1965	-60.3077	2.3506	253.8047
3	7.05	-0.564	2.1032	5.5859	-0.3075	7.0672	-0.1787	-0.7098	0.1178	0.5479	0.0561	0.0253	-0.196	-0.0337	0.1363	0.1397	0.0384	0.0293	0.274	0.0041	0.1328	-57.8572	-4.7919	265.9928
4	1.6196	0.1144	0.3606	1.9472	-0.0921	1.8226	-0.0555	-0.0954	0.0505	0.0254	-0.0124	0.016	-0.0773	-0.0482	0.0631	0.0823	0.0053	0.0039	0.0832	0.0023	0.0695	-48.6351	-4.273	255.4074
5	2.1849	0.8506	3.3834	0.9488	-0.0427	8.3079	0.0906	-0.103	-0.083	-0.0704	-0.0608	-0.0787	0.4092	-0.1811	-0.0566	0.1541	0.0097	0.0231	0.0711	-0.0017	0.1045	-47.2046	-23.7222	255.9894
6	3.5126	0.5038	-1.2716	2.4097	-0.2116	3.6229	0.0089	-0.1751	-0.0132	0.2094	-0.0392	-0.099	0.0378	-0.033	0.0369	0.0915	0.0054	-0.0136	0.0872	0.0101	0.0967	-43.9029	-14.8621	260.7772
7	3.0075	1.128	0.5794	4.057	-0.6001	1.2639	-0.0596	-0.0027	-0.3318	-0.0464	-0.0075	-0.5089	0.17	0.2435	0.0432	0.0862	0.034	0.0384	0.1148	0.0179	0.1882	-34.197	-17.9199	254.4646
8	2.3444	2.1199	0.3631	5.7597	1.9578	2.5364	0.1158	-0.0766	0.0294	0.0871	-0.1405	-0.0983	0.0067	0.0139	0.0267	0.0678	0.0218	-0.022	0.1203	0.0281	0.1047	-28.9098	-18.555	293.9321
9	0.8842	-0.1014	-0.0909	3.9672	2.1908	2.3863	0.0292	-0.0354	-0.0157	0.0109	-0.0442	-0.0969	-0.0299	0.0826	0.0174	0.0564	-0.0011	-0.012	0.1132	0.0132	0.0801	-31.5729	-12.8923	291.533
10	8.8317	-5.0475	-1.477	7.1673	1.9896	2.9538	0.0686	-0.3973	-0.3885	0.1724	0.1119	0.2248	0.2899	-0.2635	-0.1626	0.1009	-0.0305	-0.0229	0.1425	0.0623	0.1923	-48.8537	-21.3849	290.3352
11	5.852	1.0294	2.3271	1.7934	1.557	3.5079	0.0398	0.2885	-0.0858	-0.1106	-0.0181	0.2378	-0.0956	-0.1066	-0.0171	0.1038	0.0138	-0.0017	0.112	0.0207	0.1273	-49.3095	-15.2209	282.7633
12	1.4132	0.3331	0.9166	3.5313	0.3108	1.9143	0.005	0.1066	-0.0513	-0.2358	-0.0044	-0.0397	-0.0766	0.1138	0.0002	0.0786	0.0025	0.0029	0.1094	0.0044	0.0754	-38.2141	-11.7572	282.2401
13	2.6793	-0.6275	0.9748	3.6178	-1.0664	7.9595	-0.062	0.0639	0.1908	0.0634	0.026	0.176	-0.4206	-0.2171	-0.0015	0.1527	-0.0019	-0.03	0.0868	-0.0073	0.1433	-42.0101	6.4708	283.9466
14	3.5965	0.4109	1.0478	1.3758	0.5151	2.3046	-0.1328	0.1627	0.0848	-0.2051	-0.0181	0.0374	-0.1162	0.0597	0.1482	0.1518	0.0009	-0.0019	0.12	0.0208	0.0999	-40.5928	-1.9201	277.4982
15	2.3361	-1.6886	-1.3605	6.5531	1.5505	3.5915	0.0046	0.0322	0.1046	-0.3289	0.1251	-0.4195	-0.3088	0.3108	-0.1228	0.1333	-0.0402	0.0124	0.1703	0.0242	0.1403	-29.4743	2.674	278.38
16	5.4882	-0.7105	4.5129	2.0757	-1.0243	3.8147	0.2019	-0.3975	0.2842	0.0257	0.0027	0.2477	0.0699	-0.6008	-0.1872	0.1502	0.0018	0.0134	0.2105	-0.008	0.1743	-54.6572	-9.0777	257.1555
17	9.0612	3.8719	-1.7761	9.7523	-4.432	2.0471	0.2129	-0.1841	-0.0147	0.1967	0.0322	0.2292	-0.3589	0.1401	-0.2311	0.3299	-0.0381	0.0361	0.2837	-0.0433	0.231	-47.2121	-9.4036	285.2446

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 29 THROUGH 82 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 83 THROUGH 95 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 96 THROUGH 109 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 110 THROUGH 151 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 152 THROUGH 169 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 170 THROUGH 195 )
7	X-RAY DIFFRACTION	7	CHAIN 'A' AND (RESID 196 THROUGH 220 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 30 THROUGH 50 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 51 THROUGH 82 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 83 THROUGH 95 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 96 THROUGH 124 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 125 THROUGH 151 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 152 THROUGH 169 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 170 THROUGH 195 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 196 THROUGH 220 )
16	X-RAY DIFFRACTION	16	CHAIN 'D' AND (RESID 2 THROUGH 5 )
17	X-RAY DIFFRACTION	17	CHAIN 'E' AND (RESID 2 THROUGH 5 )

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About Yorodumi

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Yorodumi