PDB-5mc1: Crystal Structure of Asp276Asn mutant of Human Prolidase with Mn ...

ID or keywords:

Entry

Database: PDB / ID: 5mc1

Title

Crystal Structure of Asp276Asn 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: 1.43 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_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
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	5mc1.cif.gz	456.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5mc1.ent.gz	376 KB	Display	PDB format
PDBx/mmJSON format	5mc1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5mc1_validation.pdf.gz	472.8 KB	Display	wwPDB validaton report
Full document	5mc1_full_validation.pdf.gz	477.5 KB	Display
Data in XML	5mc1_validation.xml.gz	48.6 KB	Display
Data in CIF	5mc1_validation.cif.gz	76.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mc/5mc1 ftp://data.pdbj.org/pub/pdb/validation_reports/mc/5mc1	HTTPS FTP

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Related structure data

Related structure data	5mbyC 5mbzC 5mc0C 5mc2C 5mc3C 5mc4C 5mc5C 6h2pC 6h2qC 5m4jS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5mc5-d 6sre-d 5m4q-d 5mc3-d 6srg-d 6qsc-d 5mbz-d 5mc0-d 6h2p-d 5mby-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/m35mc1 / Data set type: diffraction image data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#205 - Jan 2017 Nuclear Pore Complex similarity (1) #235 - Jul 2019 AMPA Receptor similarity (1) #142 - Oct 2011 PDB Pioneers similarity (1)

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)	103.419, 106.848, 216.299
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-699- 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: 53885.188 Da / Num. of mol.: 2 / Mutation: D276N 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: 53885.188 Da / Num. of mol.: 2 / Mutation: D276N
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, 1309 molecules

#2: Chemical	ChemComp-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical	ChemComp-GLY / 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 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 Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1290 / 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: 2.76 Å³/Da / Density % sol: 55.49 %
Crystal grow	Temperature: 278 K / Method: vapor diffusion / pH: 7.4 / Details: 10mM NaBorate, 760mM NaCitrate

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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: 1.428→47.899 Å / Num. obs: 219713 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 7.34 % / B_iso Wilson estimate: 15.32 Å² / R_merge(I) obs: 0.098 / Net I/σ(I): 13.04
Reflection shell	Resolution: 1.43→1.51 Å / Redundancy: 7.16 % / R_merge(I) obs: 1.139 / Mean I/σ(I) obs: 1.67 / % possible all: 98.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	6.39 Å	47.9 Å
Translation	6.39 Å	47.9 Å

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j

Resolution: 1.43→47.9 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.75

	R_factor	Num. reflection	% reflection
R_free	0.157	10986	5 %
R_work	0.129	-	-
obs	0.13	219697	99.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 24.33 Å²

Refinement step

Cycle: LAST / Resolution: 1.43→47.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7548	0	89	1290	8927

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	8107
X-RAY DIFFRACTION	f_angle_d	1.215	11014
X-RAY DIFFRACTION	f_dihedral_angle_d	12.963	3062
X-RAY DIFFRACTION	f_chiral_restr	0.071	1192
X-RAY DIFFRACTION	f_plane_restr	0.006	1444

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 (%)
1.4281-1.4444	0.3328	343	0.3395	6511	X-RAY DIFFRACTION	95
1.4444-1.4614	0.308	363	0.2863	6907	X-RAY DIFFRACTION	100
1.4614-1.4792	0.2995	365	0.2726	6929	X-RAY DIFFRACTION	100
1.4792-1.4979	0.2629	364	0.2599	6905	X-RAY DIFFRACTION	100
1.4979-1.5176	0.265	367	0.2374	6975	X-RAY DIFFRACTION	100
1.5176-1.5384	0.246	359	0.2198	6828	X-RAY DIFFRACTION	100
1.5384-1.5604	0.2296	365	0.2135	6943	X-RAY DIFFRACTION	100
1.5604-1.5837	0.2323	366	0.205	6942	X-RAY DIFFRACTION	100
1.5837-1.6084	0.2277	364	0.1936	6917	X-RAY DIFFRACTION	100
1.6084-1.6348	0.2166	365	0.1869	6929	X-RAY DIFFRACTION	100
1.6348-1.663	0.2013	365	0.1737	6947	X-RAY DIFFRACTION	100
1.663-1.6932	0.1952	367	0.1647	6961	X-RAY DIFFRACTION	100
1.6932-1.7258	0.2034	366	0.1577	6953	X-RAY DIFFRACTION	100
1.7258-1.761	0.1656	363	0.1455	6903	X-RAY DIFFRACTION	100
1.761-1.7993	0.1781	364	0.143	6921	X-RAY DIFFRACTION	100
1.7993-1.8412	0.1817	366	0.1373	6957	X-RAY DIFFRACTION	100
1.8412-1.8872	0.1745	366	0.1281	6948	X-RAY DIFFRACTION	100
1.8872-1.9382	0.1552	366	0.1229	6962	X-RAY DIFFRACTION	100
1.9382-1.9953	0.1449	367	0.1178	6969	X-RAY DIFFRACTION	100
1.9953-2.0597	0.1397	368	0.1109	6987	X-RAY DIFFRACTION	100
2.0597-2.1333	0.1346	366	0.1091	6948	X-RAY DIFFRACTION	100
2.1333-2.2187	0.1452	367	0.1072	6972	X-RAY DIFFRACTION	100
2.2187-2.3197	0.1328	368	0.104	7000	X-RAY DIFFRACTION	100
2.3197-2.442	0.1299	366	0.1048	6965	X-RAY DIFFRACTION	100
2.442-2.595	0.1435	369	0.1063	7001	X-RAY DIFFRACTION	100
2.595-2.7953	0.1384	369	0.1102	7020	X-RAY DIFFRACTION	100
2.7953-3.0766	0.1338	371	0.1135	7036	X-RAY DIFFRACTION	100
3.0766-3.5216	0.1442	372	0.1066	7068	X-RAY DIFFRACTION	100
3.5216-4.4364	0.12	374	0.0932	7113	X-RAY DIFFRACTION	100
4.4364-47.9255	0.1393	385	0.1289	7294	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	1.8597	-0.7523	1.613	2.114	-1.6531	4.0307	0.0109	-0.1334	-0.1243	0.2706	0.0966	0.2612	-0.0186	-0.2403	-0.0445	0.1428	0.0061	0.0848	0.1289	0.031	0.2732	5.077	15.1981	96.5645
2	0.3142	-0.1242	-0.0342	0.7851	0.0317	0.2717	-0.0156	-0.0129	-0.0434	0.1443	0.0185	0.0456	-0.0001	-0.0286	-0.0044	0.099	0.0023	0.006	0.1215	0.0169	0.2334	16.1012	16.3295	86.7794
3	0.7711	-0.6425	-0.7898	1.4955	1.0436	1.6388	-0.0726	-0.0227	-0.1856	0.1734	0.0727	0.002	0.2075	0.0943	-0.0158	0.1147	0.0002	-0.0137	0.1172	0.0199	0.2827	22.6066	-7.7338	82.0806
4	0.9481	-0.2129	0.7072	0.5953	-0.2376	0.7156	0.128	0.2454	-0.1819	-0.0874	-0.0798	-0.1569	0.0422	0.2326	-0.0276	0.0999	0.0055	0.0006	0.1776	-0.0281	0.3567	30.4626	-8.6789	67.6294
5	1.2097	-0.2881	0.0847	0.8719	0.322	1.1676	-0.006	0.1682	-0.0589	-0.0626	-0.0695	0.1853	-0.0506	-0.2091	0.0838	0.0993	-0.0075	-0.0166	0.1551	-0.0087	0.329	8.1836	2.6728	70.1146
6	3.4472	1.2614	0.6614	1.0716	0.1683	1.0716	-0.0564	0.2355	0.1195	-0.2221	0.0514	-0.1996	-0.0919	0.1019	0.0542	0.1145	0.0113	0.0628	0.1181	0.021	0.3029	38.507	32.8587	61.9983
7	0.5832	-0.0974	-0.0292	0.9244	0.0575	0.2305	-0.002	0.024	0.0019	-0.0314	0.0225	-0.1564	0.0019	0.012	-0.0058	0.0771	0.0019	0.0008	0.125	0.0077	0.2552	31.2745	28.9765	73.7712
8	0.7363	-0.1295	-0.3325	0.7617	0.0792	0.4456	0.0355	0.1339	0.1251	-0.1075	-0.0133	0.1681	-0.076	-0.0797	0.0033	0.0912	0.0236	-0.0249	0.1504	0.033	0.3017	11.1474	45.8178	68.3975
9	1.4665	-0.7575	-0.5623	1.3309	0.3711	0.4876	-0.0283	-0.1031	0.3085	0.0932	0.0632	-0.0861	-0.0715	0.0249	-0.0246	0.1166	0.0157	-0.0102	0.1333	0.0031	0.3322	18.8787	55.5247	79.2577
10	3.9695	-0.5686	-2.0809	1.3246	-0.2001	2.5808	0.1241	-0.0667	0.2536	0.0067	-0.0464	0.1905	-0.1776	-0.0304	-0.064	0.0872	-0.0051	-0.0123	0.1028	0.003	0.319	11.2363	51.0769	73.3208
11	4.6421	-1.0826	0.3698	0.344	0.3159	1.8646	0.0528	0.791	-0.0636	-0.4384	-0.1249	0.1754	-0.0798	-0.1619	0.0206	0.2001	0.0308	-0.0562	0.2584	0.0416	0.31	7.5411	44.2751	59.4791
12	2.5477	0.6112	0.3704	6.2551	-5.2158	4.6606	0.2548	0.7576	-0.2232	0.0564	-0.309	-0.0985	-0.2832	0.6815	0.0463	0.1438	-0.0291	-0.0056	0.2952	-0.0197	0.2587	22.3089	4.3425	78.4639
13	3.4375	3.9986	-2.0217	4.6558	-2.2804	2.3576	0.1211	0.3992	-0.0795	-0.4051	-0.3526	0.1187	-0.2667	-1.2464	0.2233	0.109	0.0368	-0.0011	0.28	0.0039	0.3229	19.1601	43.136	78.3058

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 6 THROUGH 36 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 37 THROUGH 319 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 320 THROUGH 407 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 408 THROUGH 443 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 444 THROUGH 489 )
6	X-RAY DIFFRACTION	6	CHAIN 'B' AND (RESID 6 THROUGH 36 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 37 THROUGH 277 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 278 THROUGH 319 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 320 THROUGH 436 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 437 THROUGH 464 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 465 THROUGH 490 )
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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