PDB-5m4j: Crystal Structure of Wild-Type Human Prolidase with GlyPro ligand

ID or keywords:

Entry

Database: PDB / ID: 5m4j

Title

Crystal Structure of Wild-Type Human Prolidase with GlyPro ligand

Components

Xaa-Pro dipeptidase

Keywords

HYDROLASE /

prolidase /

peptidase /

hydrolysis / pita-bread /

metalloenzyme

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 / Resolution: 1.55 Å

Authors

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

Citation

Journal: FEBS J. / Year: 2017
Title: Substrate specificity and reaction mechanism of human prolidase.
Authors: Wilk, P. / Uehlein, M. / Kalms, J. / Dobbek, H. / Mueller, U. / Weiss, M.S.

History

Deposition	Oct 18, 2016	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 12, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jul 19, 2017	Group: Database references / Category: citation / citation_author Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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
Revision 1.2	Sep 20, 2017	Group: 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	Jun 2, 2021	Group: Derived calculations / Category: struct_conn Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._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	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5m4j.cif.gz	409.6 KB	Display	PDBx/mmCIF format
PDB format	pdb5m4j.ent.gz	335.7 KB	Display	PDB format
PDBx/mmJSON format	5m4j.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/m4/5m4j ftp://data.pdbj.org/pub/pdb/validation_reports/m4/5m4j	HTTPS FTP

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Related structure data

Related structure data	5m4gC 5m4lC 5m4qC 2oknS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6h2p-d 6h2q-d 5mbz-d 5mc3-d 5mc2-d 5m4g-d 6g85-d 5m4q-d 5m4l-d 5mc5-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/m35m4j / 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)	103.554, 106.942, 216.524
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	B-646- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Selection details
1	1	1	CHAIN A
2	1	1	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: 53799.094 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (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: 53799.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

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

Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 5 types, 964 molecules

#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: 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)
#4: 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)
#5: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 951 / 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: 55.7 %
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: 0.918 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2015

Radiation

Monochromator: Double Crystal Monochromator Si-11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.918 Å / Relative weight: 1

Reflection

B_iso Wilson estimate: 19.4 Å²

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.55-1.64	1.264	1.62	0.667	1	98.9
1.64-1.76	0.808	2.49	0.828	1	100
1.76-1.9	0.495	4.27	0.933	1	100
1.9-2.08	0.264	7.92	0.979	1	100
2.08-2.32	0.141	13.57	0.992	1	100
2.32-2.68	0.093	20.69	0.997	1	100
2.68-3.28	0.056	31.7	0.998	1	100
3.28-4.63	0.035	51.81	0.999	1	100
4.63-47.942	0.03	56.19	0.999	1	99.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2okn

2okn

Resolution: 1.55→47.94 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.12

	R_factor	Num. reflection	% reflection
R_free	0.168	2101	1.21 %
R_work	0.151	-	-
obs	0.151	173235	99.8 %

Solvent computation

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

Displacement parameters

B_iso mean: 30.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→47.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7542	0	58	951	8551

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7964
X-RAY DIFFRACTION	f_angle_d	1.062	10792
X-RAY DIFFRACTION	f_dihedral_angle_d	13.346	2959
X-RAY DIFFRACTION	f_chiral_restr	0.041	1167
X-RAY DIFFRACTION	f_plane_restr	0.005	1416

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Number	Refine-ID	Type
1	1	A	5503	X-RAY DIFFRACTION	POSITIONAL
1	2	B	5503	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 (%)
1.5488-1.5848	0.3131	137	0.323	11076	X-RAY DIFFRACTION	98
1.5848-1.6244	0.2723	138	0.281	11313	X-RAY DIFFRACTION	100
1.6244-1.6683	0.2611	139	0.2427	11322	X-RAY DIFFRACTION	100
1.6683-1.7174	0.2612	139	0.2267	11334	X-RAY DIFFRACTION	100
1.7174-1.7729	0.26	140	0.2118	11381	X-RAY DIFFRACTION	100
1.7729-1.8362	0.2468	139	0.198	11335	X-RAY DIFFRACTION	100
1.8362-1.9098	0.1897	140	0.1748	11422	X-RAY DIFFRACTION	100
1.9098-1.9967	0.2113	139	0.1574	11348	X-RAY DIFFRACTION	100
1.9967-2.102	0.1892	140	0.1445	11391	X-RAY DIFFRACTION	100
2.102-2.2336	0.149	140	0.1338	11405	X-RAY DIFFRACTION	100
2.2336-2.4061	0.1482	141	0.1312	11455	X-RAY DIFFRACTION	100
2.4061-2.6482	0.1383	140	0.1342	11449	X-RAY DIFFRACTION	100
2.6482-3.0314	0.1725	141	0.143	11474	X-RAY DIFFRACTION	100
3.0314-3.819	0.1341	142	0.1288	11592	X-RAY DIFFRACTION	100
3.819-47.9652	0.1406	146	0.1316	11837	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	0.4838	0.0238	0.0561	0.7768	0.2229	0.4626	0.0099	0.0508	-0.0836	-0.0716	0.0554	-0.2881	0.0253	0.0181	0.0074	0.1547	-0.0012	0.027	0.1765	-0.0116	0.2317	39.9249	25.0195	69.9225
2	0.1404	-0.0886	0.0467	0.1862	-0.3108	0.216	-0.0193	-0.0907	0.0354	0.066	0.0552	-0.3232	0.0076	0.0205	0.0042	0.149	0.0221	-0.0298	0.2125	-0.0498	0.3854	47.1137	28.8658	79.0375
3	0.5045	-0.269	-0.0394	1.0268	0.1056	-0.0645	-0.0313	-0.0216	0.0477	-0.0471	0.0188	0.0614	-0.0187	-0.0155	-0.0008	0.1586	0.009	-0.0167	0.1954	0.0088	0.1361	20.1421	34.3572	73.1473
4	0.7912	-0.3801	-0.1204	1.455	0.1983	0.1573	-0.0097	-0.0344	0.2259	-0.0089	0.0265	-0.0237	-0.049	0.0153	-0	0.1692	0.0199	-0.0121	0.1668	0.0072	0.201	17.3199	52.9377	76.3037
5	0.1022	0.0366	0.149	0.529	0.0626	0.1173	0.0467	0.1246	0.2711	-0.0883	-0.0382	0.1967	-0.0509	-0.0916	0.0065	0.1721	0.0193	0.0171	0.1825	0.0223	0.2689	10.4262	51.8019	74.3082
6	0.1815	-0.0476	0.0244	0.0584	0.0627	0.0918	-0.0004	0.4416	-0.0978	-0.4993	-0.0631	0.3203	-0.1438	-0.0102	0.1029	0.3136	0.0396	-0.1261	0.3043	0.0211	0.2572	7.5102	43.8444	59.4716
7	0.2089	0.285	0.0037	0.3756	0.1497	0.3381	0.0193	-0.0552	-0.1369	0.3912	0.0286	0.6041	-0.0105	-0.2059	-0.2409	0.3551	0.0108	0.1553	0.2193	0.0454	0.1673	5.4319	14.7983	97.1924
8	0.4523	-0.1138	-0.2075	0.3612	0.0495	0.0639	-0.0323	0.0845	0.0921	0.2428	0.0778	-0.0321	-0.0498	-0.0348	0.0383	0.2866	0.0053	-0.0066	0.1898	0.0007	0.1237	19.758	22.4845	95.555
9	0.5551	-0.1715	0.215	0.2118	0.1853	0.4496	-0.0658	0.0295	0.2646	0.4912	0.0766	0.1794	-0.2613	-0.0654	-0.2856	0.4275	0.0412	0.0886	0.2431	0.0132	0.1838	10.6401	30.7299	100.5542
10	0.1349	0.1634	0.0807	0.2149	-0.0217	0.0875	0.0633	-0.0508	-0.0158	0.3754	-0.0276	-0.3251	-0.215	0.0916	-0.0272	0.5368	0.0077	-0.0629	0.2264	-0.0292	0.0445	21.6828	21.303	105.6702
11	0.1591	-0.2214	-0.1536	0.9485	-0.1217	0.4913	-0.0329	-0.0274	-0.0784	0.3106	0.0185	0.1292	0.0323	-0.0869	-0.18	0.2444	0.0075	0.0254	0.1647	0.0147	0.1127	14.4482	12.3328	92.5458
12	0.0723	0.0193	0.0257	0.4404	0.0628	0.0102	0.0318	-0.0015	-0.0873	-0.0486	0.0068	-0.0102	0.004	0.0124	-0	0.1796	0.0096	-0.0142	0.1971	-0.0175	0.1725	18.1052	13.0616	67.348
13	0.2389	-0.2242	0.1114	0.3645	-0.0064	0.077	0.0286	0.0599	-0.1238	0.0004	-0.0623	0.1756	0.0007	-0.081	-0.001	0.165	-0.0107	-0.0091	0.1835	-0.0306	0.1829	12.8662	0.1751	70.6594
14	0.2922	-0.1836	-0.1016	0.4344	-0.0174	0.4251	-0.0345	-0.0177	-0.1696	0.2196	0.0513	-0.0102	0.1424	0.0412	-0	0.2243	-0.0004	-0.0174	0.1801	0.0014	0.2061	22.6336	-7.8477	82.1473
15	0.2216	0.0955	-0.0424	0.4139	-0.1267	0.5332	0.1025	0.0372	-0.1383	0.0209	-0.0409	-0.1869	-0.0368	0.0811	0.0424	0.1303	0.009	-0.0121	0.2049	-0.0393	0.2418	30.2103	-8.7171	67.7404
16	0.3524	0.0085	0.0135	0.6565	0.1608	0.1641	-0.0157	0.1279	-0.1229	-0.0194	-0.1022	0.2663	-0.0269	-0.0595	-0.0097	0.1457	-0.0064	-0.0225	0.2058	-0.0263	0.2109	8.3033	2.86	70.3645
17	0.6773	-1.0274	0.2167	1.6017	-0.3313	0.0708	0.0159	0.0357	0.0203	-0.0028	0.0338	0.0306	0.0259	0.031	0.0031	0.3082	0.0371	-0.086	0.388	-0.0491	0.3165	22.3957	4.5138	78.4384
18	0.0545	0.3919	0.1962	2.8522	1.4814	0.8235	-0.0108	-0.0211	-0.0151	-0.0403	0.0241	0.008	0.0741	-0.0424	-0.0102	0.2612	0.0105	-0.0199	0.3197	0.0027	0.3899	19.1702	42.982	78.3925

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 159 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 160 THROUGH 277 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 278 THROUGH 434 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 435 THROUGH 464 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 465 THROUGH 489 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 6 THROUGH 36 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 37 THROUGH 82 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 83 THROUGH 124 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 125 THROUGH 159 )
11	X-RAY DIFFRACTION	11	CHAIN 'B' AND (RESID 160 THROUGH 212 )
12	X-RAY DIFFRACTION	12	CHAIN 'B' AND (RESID 213 THROUGH 277 )
13	X-RAY DIFFRACTION	13	CHAIN 'B' AND (RESID 278 THROUGH 319 )
14	X-RAY DIFFRACTION	14	CHAIN 'B' AND (RESID 320 THROUGH 407 )
15	X-RAY DIFFRACTION	15	CHAIN 'B' AND (RESID 408 THROUGH 443 )
16	X-RAY DIFFRACTION	16	CHAIN 'B' AND (RESID 444 THROUGH 489 )
17	X-RAY DIFFRACTION	17	CHAIN 'C' AND (RESID 1 THROUGH 2 )
18	X-RAY DIFFRACTION	18	CHAIN 'D' AND (RESID 1 THROUGH 2 )

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Yorodumi