PDB-5mc5: Crystal Structure of delGlu452 mutant of Human Prolidase with Mn ...

ID or keywords:

Entry

Database: PDB / ID: 5mc5

Title

Crystal Structure of delGlu452 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 / amino acid metabolic process / negative regulation of programmed cell death / metalloaminopeptidase activity / collagen catabolic process / metallocarboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / extracellular exosome
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 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 / struct_conn Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
Revision 1.5	Nov 13, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5mc5.cif.gz	428 KB	Display	PDBx/mmCIF format
PDB format	pdb5mc5.ent.gz	351.4 KB	Display	PDB format
PDBx/mmJSON format	5mc5.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5mc5_validation.pdf.gz	475.1 KB	Display	wwPDB validaton report
Full document	5mc5_full_validation.pdf.gz	477 KB	Display
Data in XML	5mc5_validation.xml.gz	43.6 KB	Display
Data in CIF	5mc5_validation.cif.gz	67 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mc/5mc5 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/5mc5	HTTPS FTP

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Related structure data

Related structure data	5mbyC 5mbzC 5mc0C 5mc1C 5mc2C 5mc3C 5mc4C 6h2pC 6h2qC 5m4jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5mc1-d 5mc3-d 5mbz-d 5m4q-d 6h2p-d 6h2q-d 5mby-d 6sre-d 5mc0-d 5mc2-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/m35mc5 / 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

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	103.779, 108.043, 211.341
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1
1	2
2	2

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A
2	1	1	CHAIN B
1	1	2	CHAIN A
2	1	2	CHAIN B

NCS ensembles :

ID
1
2

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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: 53106.340 Da / Num. of mol.: 2 / Mutation: delE452 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: 53106.340 Da / Num. of mol.: 2 / Mutation: delE452
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 , 6 types, 973 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 Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical	ChemComp-GLY / GLYCINE Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₅NO₂ / Source: (synth.) Homo sapiens (human)
#5: Chemical	ChemComp-PRO / PROLINE Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₉NO₂ / Source: (synth.) Homo sapiens (human)
#6: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 961 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 2.78 Å³/Da / Density % sol: 55.75 %
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: May 23, 2015
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: 1.899→48.1 Å / Num. obs: 93478 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.75 % / B_iso Wilson estimate: 28.17 Å² / R_merge(I) obs: 0.114 / Net I/σ(I): 12.9
Reflection shell	Resolution: 1.9→2.01 Å / Redundancy: 6.67 % / R_merge(I) obs: 1.022 / Mean I/σ(I) obs: 1.75 / % possible all: 98.8

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j

Resolution: 1.9→46.58 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.09

	R_factor	Num. reflection	% reflection
R_free	0.181	2101	2.25 %
R_work	0.148	-	-
obs	0.148	93464	99.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 32.93 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→46.58 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7433	0	42	961	8436

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	7783
X-RAY DIFFRACTION	f_angle_d	0.886	10552
X-RAY DIFFRACTION	f_dihedral_angle_d	12.9	2884
X-RAY DIFFRACTION	f_chiral_restr	0.035	1147
X-RAY DIFFRACTION	f_plane_restr	0.004	1387

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	5366	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5366	X-RAY DIFFRACTION	POSITIONAL
2	1	A	14	X-RAY DIFFRACTION	POSITIONAL
2	2	B	14	X-RAY DIFFRACTION	POSITIONAL

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 (%)
1.8985-1.9427	0.2964	134	0.2791	5843	X-RAY DIFFRACTION	97
1.9427-1.9913	0.3036	140	0.2485	6058	X-RAY DIFFRACTION	100
1.9913-2.0451	0.2534	138	0.2274	6032	X-RAY DIFFRACTION	100
2.0451-2.1053	0.258	140	0.2073	6061	X-RAY DIFFRACTION	100
2.1053-2.1732	0.2331	139	0.1886	6064	X-RAY DIFFRACTION	100
2.1732-2.2509	0.2159	140	0.1788	6079	X-RAY DIFFRACTION	100
2.2509-2.341	0.1975	139	0.1697	6054	X-RAY DIFFRACTION	100
2.341-2.4476	0.2226	139	0.1572	6069	X-RAY DIFFRACTION	100
2.4476-2.5766	0.1955	141	0.1551	6110	X-RAY DIFFRACTION	100
2.5766-2.738	0.1824	139	0.1465	6054	X-RAY DIFFRACTION	100
2.738-2.9494	0.1905	140	0.1381	6100	X-RAY DIFFRACTION	100
2.9494-3.2461	0.141	142	0.1261	6146	X-RAY DIFFRACTION	100
3.2461-3.7157	0.1397	141	0.1147	6148	X-RAY DIFFRACTION	100
3.7157-4.6807	0.13	142	0.1081	6192	X-RAY DIFFRACTION	100
4.6807-46.5909	0.1887	147	0.1501	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	1.0746	0.0739	0.14	0.9878	-0.4264	1.3318	0.0272	-0.0688	0.1765	0.2594	0.0189	0.1615	-0.2797	-0.1482	-0.0529	0.3146	0.0445	0.0422	0.2592	0.0101	0.2845	11.3444	23.8317	95.814
2	0.65	0.067	0.4393	1.0176	0.06	2.1446	0.0141	-0.1312	0.0259	0.2326	0.0178	0.0789	-0.1904	0.0194	-0.041	0.2725	0.0204	0.0318	0.2338	0.016	0.2681	16.0877	16.0089	95.1552
3	0.6262	0.0925	-0.5672	1.5807	0.6589	1.59	-0.0317	-0.1066	-0.1284	-0.0245	0.1063	-0.1463	0.1297	0.1722	-0.0624	0.2808	0.0417	-0.0324	0.2592	0.0168	0.2919	18.1941	14.536	65.275
4	0.6557	-0.1842	-0.2115	1.0321	0.4475	1.4363	0.0106	-0.0216	-0.2029	0.0183	0.0494	-0.039	0.1596	0.1478	-0.0517	0.2216	0.0352	-0.0409	0.2136	0.0079	0.2811	21.5543	-4.6649	73.0809
5	1.0831	1.1125	-0.6431	1.2157	0.0241	7.4406	-0.0607	0.1329	-0.0523	-0.1307	0.0697	0.3751	-0.1856	-0.6147	-0.0089	0.2422	0.0444	-0.0664	0.2886	0.001	0.4219	5.1916	1.2945	68.664
6	1.1622	0.1461	0.1896	0.7449	0.0131	0.7897	0.0014	0.0209	-0.1735	-0.0571	0.0121	-0.2369	0.1243	0.0964	-0.0159	0.228	0.0526	0.0245	0.2247	-0.0018	0.309	39.7548	25.9981	69.3035
7	1.702	-0.6889	0.2436	1.9986	0.0967	1.038	-0.1422	-0.2302	0.038	0.2584	0.1487	-0.3216	0.068	0.1777	0.0048	0.2265	0.04	-0.013	0.2796	-0.0105	0.3562	46.4353	32.6304	78.5375
8	2.3983	0.1069	-0.7141	0.7193	-0.2237	0.5969	-0.0231	-0.1737	0.1171	0.0229	0.052	0.1465	-0.0391	0	-0.024	0.2708	0.0627	-0.0195	0.2386	0.0231	0.2964	11.7933	34.8898	69.6226
9	1.7022	-0.3667	-0.1783	1.3231	0.0765	0.6809	0.0007	-0.1255	0.2945	0.0417	0.0282	0.0518	-0.1968	-0.0528	-0.033	0.2694	0.0662	0.0041	0.2111	0.0042	0.2891	17.7417	52.7452	74.212
10	1.2817	-0.0351	0.5432	3.0359	1.4514	3.4726	-0.0224	-0.3472	0.1663	0.5811	-0.1191	0.4778	-0.2192	-0.4593	0.1531	0.4073	0.0773	0.0838	0.3541	-0.0148	0.3957	4.1052	56.5302	85.0795
11	7.4053	1.6153	0.3136	0.6569	0.0565	0.6949	-0.2109	0.4167	0.0487	-0.313	0.1498	0.0568	-0.0686	-0.0912	0.0648	0.4026	0.0626	-0.0054	0.242	0.0409	0.3164	13.3705	46.8786	59.9467
12	3.2377	-3.7416	1.4055	9.6045	-2.5477	2.5225	-0.1309	0.0287	0.0408	-0.0441	0.2131	0.0146	0.0328	0.2349	-0.0783	0.3861	0.0818	-0.1228	0.7435	-0.069	0.5213	21.9568	5.4873	76.2584
13	0.6034	1.861	1.2592	8.7979	7.4629	6.8179	0.008	-0.1442	0.0149	-0.1323	0.1617	0.0214	0.1429	-0.0323	-0.1764	0.4688	0.1091	-0.0278	0.564	0.0369	0.6334	18.7581	44.0108	77.5972

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 6 THROUGH 124 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 125 THROUGH 212 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 213 THROUGH 277 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 278 THROUGH 452 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 453 THROUGH 482 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 6 THROUGH 124 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 125 THROUGH 188 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 189 THROUGH 271 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 272 THROUGH 418 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 419 THROUGH 452 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 453 THROUGH 483 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 1 THROUGH 2 )
13	X-RAY DIFFRACTION	13	CHAIN 'D' AND (RESID 1 THROUGH 2 )

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