PDB-5mbz: Crystal Structure of Ser202Phe mutant of Human Prolidase with Mn ...

ID or keywords:

Entry

Database: PDB / ID: 5mbz

Title

Crystal Structure of Ser202Phe mutant of Human Prolidase with Mn ions and GlyPro ligand

Components

Xaa-Pro dipeptidase

Keywords

HYDROLASE /

prolidase /

peptidase /

hydrolysis / pita-bread /

metalloenzyme /

mutation

Function / homology

Function and homology information

Xaa-Pro dipeptidase /

proline dipeptidase activity / negative regulation of programmed cell death / amino acid metabolic process / metalloaminopeptidase activity / collagen catabolic process /

metallocarboxypeptidase activity / manganese ion binding /

peptidase activity /

proteolysis / extracellular exosome
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.5 Å

Authors

Wilk, P. / Mueller, U. / Dobbek, H. / Weiss, M.S.

Citation

Journal: FEBS J. / Year: 2018
Title: Structural basis for prolidase deficiency disease mechanisms.
Authors: Wilk, P. / Uehlein, M. / Piwowarczyk, R. / Dobbek, H. / Mueller, U. / Weiss, M.S.

History

Deposition	Nov 9, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 20, 2017	Provider: repository / Type: Initial release
Revision 1.1	Aug 15, 2018	Group: Data collection / Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2	Sep 26, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3	Apr 22, 2020	Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4	Jan 17, 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 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mbz.cif.gz	444 KB	Display	PDBx/mmCIF format
PDB format	pdb5mbz.ent.gz	364.1 KB	Display	PDB format
PDBx/mmJSON format	5mbz.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mb/5mbz ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mbz	HTTPS FTP

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Related structure data

Related structure data	5mbyC 5mc0C 5mc1C 5mc2C 5mc3C 5mc4C 5mc5C 6h2pC 6h2qC 5m4jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6h2p-d 5mc2-d 5mby-d 5mc5-d 5mc0-d 6srf-d 5m4q-d 6h2q-d 5mc3-d 5mc1-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.18430/m35mbz / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1) #262 - Oct 2021 Fifty Years of Open Access to PDB Structures similarity (1) #57 - Sep 2004 Catalase similarity (1) #205 - Jan 2017 Nuclear Pore Complex similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (2)

Deposited unit

A: Xaa-Pro dipeptidase

B: Xaa-Pro dipeptidase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	103.785, 106.945, 216.316
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-730- HOH

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Protein , 1 types, 2 molecules AB

#1: Protein	Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Peptidase D / Proline dipeptidase / Prolidase Mass: 53859.191 Da / Num. of mol.: 2 / Mutation: S202F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase

#1: Protein

Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Peptidase D / Proline dipeptidase / Prolidase

Mass: 53859.191 Da / Num. of mol.: 2 / Mutation: S202F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host:

Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 8 types, 1143 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-OH / HYDROXIDE ION / Hydroxide Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical	ChemComp-GLY / GLYCINE / Glycine Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂ / Details: Substrate / Source: (synth.) Homo sapiens (human)
#5: Chemical	ChemComp-PRO / PROLINE / Proline Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₂ / Details: Substrate / Source: (synth.) Homo sapiens (human)
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1126 / 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: 2.78 Å³/Da / Density % sol: 55.71 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 10mM NaBorate, 690-760mM NaCitrate / PH range: 7.6-8.2

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 14, 2014
Radiation	Monochromator: Double Crystal Monochromator Si-11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 1.499→47.934 Å / Num. obs: 191294 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.41 % / B_iso Wilson estimate: 18.01 Å² / R_merge(I) obs: 0.082 / Net I/σ(I): 14.73
Reflection shell	Resolution: 1.5→1.59 Å / Redundancy: 7.56 % / R_merge(I) obs: 1.1 / Mean I/σ(I) obs: 1.87 / % possible all: 99.5

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	8.11 Å	47.93 Å
Translation	8.11 Å	47.93 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.9_1692	refinement
PHASER	2.5.6	phasing
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
XSCALE		data scaling
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j

Resolution: 1.5→46.79 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.18

	R_factor	Num. reflection	% reflection
R_free	0.175	9565	5 %
R_work	0.15	-	-
obs	0.151	191280	99.9 %

Solvent computation

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

Displacement parameters

B_iso mean: 26.81 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→46.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7477	0	57	1126	8660

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	7922
X-RAY DIFFRACTION	f_angle_d	1.24	10747
X-RAY DIFFRACTION	f_dihedral_angle_d	13.358	2955
X-RAY DIFFRACTION	f_chiral_restr	0.074	1166
X-RAY DIFFRACTION	f_plane_restr	0.007	1409

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 (%)
1.4992-1.5162	0.2774	311	0.277	5903	X-RAY DIFFRACTION	98
1.5162-1.5341	0.3105	314	0.2692	5982	X-RAY DIFFRACTION	100
1.5341-1.5528	0.298	320	0.2583	6073	X-RAY DIFFRACTION	100
1.5528-1.5724	0.2837	314	0.2427	5962	X-RAY DIFFRACTION	100
1.5724-1.5931	0.2617	317	0.2378	6019	X-RAY DIFFRACTION	100
1.5931-1.615	0.2745	317	0.2347	6021	X-RAY DIFFRACTION	100
1.615-1.638	0.2419	315	0.2253	6000	X-RAY DIFFRACTION	100
1.638-1.6625	0.2579	320	0.2178	6067	X-RAY DIFFRACTION	100
1.6625-1.6885	0.2406	316	0.2058	6001	X-RAY DIFFRACTION	100
1.6885-1.7161	0.2425	315	0.1997	6001	X-RAY DIFFRACTION	100
1.7161-1.7457	0.1973	319	0.1915	6044	X-RAY DIFFRACTION	100
1.7457-1.7775	0.2145	317	0.1785	6038	X-RAY DIFFRACTION	100
1.7775-1.8117	0.2083	318	0.17	6034	X-RAY DIFFRACTION	100
1.8117-1.8487	0.2054	317	0.169	6026	X-RAY DIFFRACTION	100
1.8487-1.8889	0.2177	317	0.1622	6027	X-RAY DIFFRACTION	100
1.8889-1.9328	0.1839	318	0.1595	6041	X-RAY DIFFRACTION	100
1.9328-1.9811	0.1729	318	0.1537	6030	X-RAY DIFFRACTION	100
1.9811-2.0347	0.1666	319	0.1414	6076	X-RAY DIFFRACTION	100
2.0347-2.0946	0.1706	317	0.1368	6014	X-RAY DIFFRACTION	100
2.0946-2.1622	0.1694	320	0.1372	6082	X-RAY DIFFRACTION	100
2.1622-2.2395	0.163	318	0.1325	6036	X-RAY DIFFRACTION	100
2.2395-2.3291	0.1582	321	0.1298	6112	X-RAY DIFFRACTION	100
2.3291-2.4351	0.1338	318	0.1233	6042	X-RAY DIFFRACTION	100
2.4351-2.5635	0.1693	321	0.1303	6090	X-RAY DIFFRACTION	100
2.5635-2.7241	0.1595	320	0.135	6081	X-RAY DIFFRACTION	100
2.7241-2.9344	0.1743	320	0.1338	6082	X-RAY DIFFRACTION	100
2.9344-3.2296	0.162	324	0.134	6156	X-RAY DIFFRACTION	100
3.2296-3.6968	0.1483	322	0.1278	6124	X-RAY DIFFRACTION	100
3.6968-4.6569	0.1417	327	0.1206	6198	X-RAY DIFFRACTION	100
4.6569-46.809	0.1702	335	0.1652	6353	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	0.4567	-0.0448	0.0359	1.0508	-0.2471	0.7436	-0.0031	-0.0562	0.0376	0.3203	0.013	0.058	-0.1008	-0.0369	-0.0117	0.2439	0.0088	0.035	0.1664	0.0036	0.1321	14.5178	19.9504	94.1789
2	2.4747	-0.9447	-0.5863	1.0748	-0.0464	0.2085	0.1452	-0.4375	0.3245	0.2329	0.1227	-0.3594	-0.1359	0.2075	-0.2417	0.3485	-0.0392	0.023	0.2769	-0.0514	0.2961	22.5229	11.6076	66.8935
3	0.6534	-0.2642	-0.1862	1.3654	0.5116	0.998	0.0008	0.025	-0.1027	0.0788	0.0219	-0.0651	0.057	0.0556	-0.0241	0.1106	-0.01	-0.0016	0.1325	-0.0014	0.1268	21.8226	-5.1573	75.6997
4	1.3745	0.4383	-0.4823	1.3626	-0.1813	1.8584	-0.062	0.2039	0.0671	-0.0381	-0.0312	0.2777	-0.1335	-0.2835	0.0786	0.1315	0.003	-0.016	0.1807	-0.0262	0.1822	8.4332	3.0259	70.3112
5	0.9067	0.0976	0.0426	1.0351	0.1387	0.4289	-0.0022	0.0185	-0.0728	-0.0712	0.0512	-0.2451	0.0157	0.0507	-0.0449	0.1338	0.0049	0.0239	0.1409	-0.0017	0.164	36.5553	28.5766	71.2599
6	0.0279	0.0622	0.117	0.0755	0.0286	1.7608	-0.2633	-0.3865	-0.1048	0.3197	0.165	-0.1886	0.1821	0.4787	0.0537	0.3177	0.0302	0.0149	0.3465	0.0894	0.5042	12.0362	34.7361	78.5856
7	1.3201	-0.3264	-0.1444	1.3246	0.0821	0.4175	-0.0251	-0.1269	0.1842	0.0179	0.0368	0.1372	-0.0878	-0.0396	-0.0155	0.1404	0.0229	-0.0054	0.1502	0.0071	0.1687	15.9431	51.8328	76.4075
8	2.3832	0.266	-0.1297	1.0972	-0.2787	0.5807	0.0944	0.1798	0.2344	-0.2439	0.0036	0.3058	-0.0471	-0.1303	-0.0911	0.2029	0.0212	-0.0489	0.1692	0.0444	0.2439	9.0729	48.0129	67.237
9	2.0002	2.0002	2.0001	2.0001	2	2	-0.1871	0.3055	-0.0536	-0.1295	0.0453	0.0147	-0.1266	-0.0322	0.1418	0.1178	-0.0141	-0.0234	0.1903	0.0317	0.1803	22.5576	4.6045	78.3683
10	1.9999	2	2.0001	2.0001	1.9997	2.0002	0.1779	0.0486	-0.1917	-0.0504	0.1324	-0.0344	-0.1399	-0.2799	-0.318	0.1859	-0.0234	0.0468	0.2186	0.0098	0.2359	19.4865	43.2333	78.3671

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 8 THROUGH 236 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 237 THROUGH 273 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 274 THROUGH 445 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 446 THROUGH 491 )
5	X-RAY DIFFRACTION	5	CHAIN 'B' AND (RESID 8 THROUGH 236 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 237 THROUGH 266 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 267 THROUGH 438 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 439 THROUGH 490 )
9	X-RAY DIFFRACTION	9	CHAIN 'C' AND (RESID 1 THROUGH 2 )
10	X-RAY DIFFRACTION	10	CHAIN 'D' AND (RESID 1 THROUGH 2 )

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