PDB-5z48: Crystal structure of pyrrolidone carboxylate peptidase I from Dei...

ID or keywords:

Entry

Database: PDB / ID: 5z48

Title

Crystal structure of pyrrolidone carboxylate peptidase I from Deinococcus radiodurans R1 bound to pyroglutamate

Components

Pyrrolidone-carboxylate peptidase

Keywords

HYDROLASE / omega peptidase / pyroglutamate / exopeptidase

Function / homology

Function and homology information

pyroglutamyl-peptidase I / pyroglutamyl-peptidase activity / proteolysis / cytosol
Similarity search - Function

Biological species

Deinococcus radiodurans R1 (radioresistant)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.551 Å

Authors

Agrawal, R. / Kumar, A. / Kumar, A. / Makde, R.D.

Citation

Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures of pyrrolidone-carboxylate peptidase I from Deinococcus radiodurans reveal the mechanism of L-pyroglutamate recognition.
Authors: Agrawal, R. / Singh, R. / Kumar, A. / Kumar, A. / Makde, R.D.

History

Deposition	Jan 10, 2018	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Apr 17, 2019	Group: Data collection / 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Nov 22, 2023	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.ptnr2_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5z48.cif.gz	184.7 KB	Display	PDBx/mmCIF format
PDB format	pdb5z48.ent.gz	145.9 KB	Display	PDB format
PDBx/mmJSON format	5z48.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	5z48_validation.pdf.gz	466.4 KB	Display	wwPDB validaton report
Full document	5z48_full_validation.pdf.gz	468.2 KB	Display
Data in XML	5z48_validation.xml.gz	22.6 KB	Display
Data in CIF	5z48_validation.cif.gz	34.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/z4/5z48 ftp://data.pdbj.org/pub/pdb/validation_reports/z4/5z48	HTTPS FTP

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Related structure data

Related structure data	5z47C 5z40S S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5z40-1 5z47-1 6jr6-3 6jr7-2 3lx6-d 2qez-4 6jr6-4 5nn4-d 6jr8-3 5nn5-d 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

Deposited unit

A: Pyrrolidone-carboxylate peptidase

B: Pyrrolidone-carboxylate peptidase

hetero molecules

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

1

A: Pyrrolidone-carboxylate peptidase

B: Pyrrolidone-carboxylate peptidase

hetero molecules

A: Pyrrolidone-carboxylate peptidase

B: Pyrrolidone-carboxylate peptidase

hetero molecules

defined by author&software
Evidence: gel filtration
94.1 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	89.069, 46.918, 105.584
Angle α, β, γ (deg.)	90.00, 105.51, 90.00
Int Tables number	5
Space group name H-M	I121

#1: Protein	Pyrrolidone-carboxylate peptidase / 5-oxoprolyl-peptidase / Pyroglutamyl-peptidase I / Pyrase Mass: 23261.492 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans R1 (radioresistant) Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422 Gene: pcp, DR_0490 / Plasmid: pET50-STR / Details (production host): pET3a based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta / References: UniProt: Q9RX25, pyroglutamyl-peptidase I
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical	ChemComp-DMS / DIMETHYL SULFOXIDE Mass: 78.133 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C₂H₆OS / Comment: DMSO, precipitant*YM
#4: Chemical	ChemComp-PCA / PYROGLUTAMIC ACID Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₇NO₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 481 / 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: 2.28 Å³/Da / Density % sol: 46.16 %
Crystal grow	Temperature: 294 K / Method: microbatch / pH: 6.5 / Details: 0.2M NaCl, 0.1M Bis-tris pH 6.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Oct 11, 2017 / Details: Mirrors
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97947 Å / Relative weight: 1
Reflection	Resolution: 1.55→42.91 Å / Num. obs: 59905 / % possible obs: 98 % / Redundancy: 3.5 % / B_iso Wilson estimate: 10.2 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.034 / R_pim(I) all: 0.019 / R_rim(I) all: 0.04 / Net I/σ(I): 22
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.304 / Mean I/σ(I) obs: 3 / Num. unique obs: 2297 / CC_1/2: 0.85 / R_pim(I) all: 0.228 / R_rim(I) all: 0.382 / % possible all: 77

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Processing

Software

Name	Version	Classification
PHENIX	(1.10.1_2155: ???)	refinement
Coot		model building
PHENIX		model building
PHASER		phasing
Aimless		data scaling
XDS		data reduction
MAR345dtb		data collection

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5Z40

5z40

Resolution: 1.551→34.22 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.92

	R_factor	Num. reflection	% reflection
R_free	0.1864	2940	4.91 %
R_work	0.1585	-	-
obs	0.1599	59895	97.98 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.551→34.22 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3161	0	32	481	3674

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.012	3344
X-RAY DIFFRACTION	f_angle_d	1.17	4603
X-RAY DIFFRACTION	f_dihedral_angle_d	13.325	1990
X-RAY DIFFRACTION	f_chiral_restr	0.077	518
X-RAY DIFFRACTION	f_plane_restr	0.009	618

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 (%)
1.551-1.5765	0.2403	113	0.2564	2069	X-RAY DIFFRACTION	76
1.5765-1.6037	0.2547	136	0.189	2749	X-RAY DIFFRACTION	100
1.6037-1.6328	0.2225	147	0.1828	2738	X-RAY DIFFRACTION	100
1.6328-1.6642	0.187	135	0.17	2750	X-RAY DIFFRACTION	100
1.6642-1.6982	0.1894	140	0.1691	2731	X-RAY DIFFRACTION	99
1.6982-1.7351	0.2152	150	0.1753	2748	X-RAY DIFFRACTION	99
1.7351-1.7755	0.2089	122	0.1779	2742	X-RAY DIFFRACTION	99
1.7755-1.8199	0.2122	144	0.1685	2712	X-RAY DIFFRACTION	99
1.8199-1.8691	0.2066	140	0.1638	2745	X-RAY DIFFRACTION	99
1.8691-1.9241	0.1826	129	0.1647	2727	X-RAY DIFFRACTION	99
1.9241-1.9862	0.1796	149	0.1578	2692	X-RAY DIFFRACTION	98
1.9862-2.0572	0.2007	144	0.1564	2735	X-RAY DIFFRACTION	99
2.0572-2.1395	0.1846	134	0.1558	2744	X-RAY DIFFRACTION	98
2.1395-2.2369	0.2006	157	0.1497	2685	X-RAY DIFFRACTION	98
2.2369-2.3548	0.1722	138	0.1443	2731	X-RAY DIFFRACTION	99
2.3548-2.5023	0.1497	149	0.1473	2692	X-RAY DIFFRACTION	99
2.5023-2.6954	0.1908	147	0.1593	2755	X-RAY DIFFRACTION	99
2.6954-2.9665	0.2219	124	0.1626	2769	X-RAY DIFFRACTION	99
2.9665-3.3954	0.1905	145	0.1533	2757	X-RAY DIFFRACTION	99
3.3954-4.2766	0.1626	134	0.1492	2833	X-RAY DIFFRACTION	100
4.2766-34.2283	0.1633	163	0.1529	2851	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	3.6014	-4.199	1.0714	5.3979	-1.4603	2.8441	0.1274	-0.0639	-0.0284	-0.0395	-0.1191	-0.2147	0.1021	0.3602	-0.0569	0.1035	-0.0237	-0.0039	0.1436	-0.0088	0.1112	-10.4559	-16.0577	8.6828
2	8.5859	-5.9834	5.8167	6.8543	-4.7737	6.1727	-0.2165	-0.2953	0.0978	0.2982	0.2271	0.0995	-0.451	-0.2538	-0.0504	0.1571	-0.0142	0.0224	0.1167	-0.0182	0.1272	-26.3493	-9.1223	10.8118
3	3.0688	-1.9559	2.4589	2.7324	-2.3992	5.4485	-0.1067	-0.0065	0.0597	0.1802	-0.0799	-0.2758	-0.0604	0.2871	0.1477	0.0878	-0.0334	-0.0007	0.0998	-0.0019	0.1184	-13.3803	-14.5093	10.9834
4	7.0579	-5.7546	2.6049	8.8324	-2.8361	3.361	-0.1105	-0.0335	0.2508	0.1369	-0.0113	-0.3729	-0.3154	0.253	0.1052	0.1189	-0.0592	0.0028	0.1592	-0.0037	0.1166	-10.9953	-7.1073	0.5136
5	1.5788	0.2859	0.0907	1.4526	-0.4375	1.6077	0.0181	0.0353	0.0253	-0.0072	0.0056	-0.0088	0.0135	0.0573	-0.03	0.074	0.0002	0.0105	0.0627	-0.0037	0.0688	-23.1973	-19.6821	1.9067
6	2.7145	-3.498	-2.4119	7.7238	5.8289	5.7762	-0.0057	0.1299	0.2027	-0.116	-0.0718	0.0509	-0.483	-0.0334	0.0652	0.1539	-0.0123	-0.0191	0.1063	0.035	0.1223	-27.1646	-5.3767	-9.6443
7	1.203	-0.5042	0.2605	1.1483	-0.6101	2.7226	0.0158	-0.0052	-0.0204	-0.0771	-0.016	0.0073	0.1193	0.11	0.0082	0.0771	-0.0091	-0.0077	0.0569	-0.0236	0.0708	-22.5138	-24.2783	-0.735
8	7.9161	0.3401	1.8099	1.9824	-1.6648	2.0955	0.0031	0.335	0.1038	-0.0404	-0.0377	-0.0928	0.0603	0.312	0.0426	0.1128	-0.0177	0.0051	0.1128	-0.0075	0.0612	-13.9949	-14.2337	-6.3821
9	1.5835	-0.0818	-1.6592	1.1158	0.1719	2.6004	0.1217	0.0202	0.0758	0.0022	-0.0528	0.1227	-0.191	-0.0982	-0.0538	0.0942	0.0079	-0.0065	0.0577	0.004	0.0799	-30.9071	-15.2487	6.426
10	7.6555	-4.863	-2.497	6.6838	1.537	5.0361	-0.0122	-0.1497	0.089	0.1115	0.0585	-0.2693	0.1357	0.3196	-0.0424	0.0869	-0.0338	-0.0226	0.0814	-0.0039	0.0769	-19.8288	-24.1129	12.7132
11	3.5122	0.757	-0.6459	3.8509	-2.4524	4.9174	-0.0146	0.0765	-0.2012	-0.1429	0.0311	0.0815	0.0993	-0.0975	0.0122	0.1265	-0.0009	-0.0035	0.0607	-0.0561	0.1066	-41.7334	-31.4122	-25.4584
12	2.8158	-0.1456	1.5975	1.4161	-0.5375	4.1043	0.0776	0.3321	0.0337	-0.3753	-0.0297	0.155	0.1407	0.1203	-0.0547	0.136	0.0012	0.0085	0.1237	-0.0285	0.0866	-39.2748	-28.3214	-32.6722
13	2.5116	1.9353	-2.4279	4.3317	-2.9653	3.7645	0.0138	0.2381	-0.2189	-0.4877	-0.0293	-0.1344	0.3069	0.3719	-0.0405	0.1669	0.0135	0.0198	0.1442	-0.0605	0.1316	-28.7279	-35.4302	-29.6239
14	0.5205	-0.1448	0.5388	1.7492	-0.0665	1.2352	-0.0678	0.0416	0.0142	-0.0457	0.046	-0.0153	-0.0177	0.0572	0.0271	0.0726	-0.0055	0.0072	0.0764	-0.0113	0.0729	-35.9236	-23.095	-19.7044
15	6.4088	6.5471	1.2512	7.5305	0.5936	2.377	0.2211	-0.0595	-0.3696	0.0764	-0.0473	-0.1165	0.3903	0.1017	-0.1692	0.1765	0.0435	-0.0261	0.0978	-0.006	0.1385	-27.6648	-37.3637	-10.7492
16	2.0628	0.0949	0.7021	0.8389	-0.474	1.9474	-0.0469	0.0826	0.041	0.0197	0.0122	-0.0357	-0.0284	0.0363	0.0457	0.0891	-0.0122	0.0056	0.0531	-0.0271	0.0638	-33.327	-18.4962	-19.0918
17	4.3463	0.219	-2.664	3.1736	-0.9747	5.6946	-0.0656	0.1885	-0.1129	-0.1279	0.0522	-0.2547	0.164	0.21	0.021	0.0779	0.0088	0.0016	0.0903	-0.0341	0.0959	-24.7363	-28.3903	-23.3238
18	3.6353	0.2312	-0.7382	0.9765	0.1688	0.6621	0.0206	-0.1434	-0.237	0.0668	-0.0457	0.0301	0.0151	0.0275	0.0737	0.1008	0.0034	-0.009	0.062	0.0111	0.094	-42.4707	-27.6117	-16.0006
19	4.3963	2.7085	-2.3546	6.8884	-1.9454	5.3953	-0.1064	0.2314	0.1452	-0.3439	0.1168	0.0131	-0.1716	-0.0116	0.0102	0.1038	0.0143	-0.0279	0.0778	-0.0081	0.0619	-43.4148	-18.3356	-28.2454

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 9 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 10 through 27 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 28 through 46 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 47 through 61 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 62 through 85 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 86 through 105 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 106 through 142 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 143 through 158 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 159 through 191 )
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 192 through 210 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid -1 through 27 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 28 through 46 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 47 through 61 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 62 through 85 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 86 through 105 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 106 through 142 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 143 through 157 )
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 158 through 191 )
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 192 through 211 )

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