PDB-5jwg: Crystal structure of Porphyromonas endodontalis DPP11 in complex ...

ID or keywords:

Entry

Database: PDB / ID: 5jwg

Title

Crystal structure of Porphyromonas endodontalis DPP11 in complex with dipeptide Arg-Asp

Components

Asp/Glu-specific dipeptidyl-peptidase

Keywords

HYDROLASE / peptidase / bacterial enzyme / dipeptide

Function / homology

Function and homology information

Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / serine-type aminopeptidase activity / dipeptidyl-peptidase activity / peptide catabolic process / cell surface / proteolysis / extracellular region
Similarity search - Function

Biological species

Porphyromonas endodontalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Bezerra, G.A. / Fedosyuk, S. / Ohara-Nemoto, Y. / Nemoto, T.K. / Djinovic-Carugo, K.

Citation

Journal: Sci Rep / Year: 2017
Title: Bacterial protease uses distinct thermodynamic signatures for substrate recognition.
Authors: Bezerra, G.A. / Ohara-Nemoto, Y. / Cornaciu, I. / Fedosyuk, S. / Hoffmann, G. / Round, A. / Marquez, J.A. / Nemoto, T.K. / Djinovic-Carugo, K.

History

Deposition	May 12, 2016	Deposition site: RCSB / Processing site: PDBE
Revision 1.0	Jun 14, 2017	Provider: repository / Type: Initial release
Revision 1.1	Jun 21, 2017	Group: Database references / Category: citation Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Nov 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5jwg.cif.gz	568.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	5jwg_validation.pdf.gz	485.5 KB	Display	wwPDB validaton report
Full document	5jwg_full_validation.pdf.gz	502.5 KB	Display
Data in XML	5jwg_validation.xml.gz	53 KB	Display
Data in CIF	5jwg_validation.cif.gz	75 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jw/5jwg ftp://data.pdbj.org/pub/pdb/validation_reports/jw/5jwg	HTTPS FTP

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Related structure data

Related structure data	5jwfC 5jwiC 5jxfC 5jxkC 5jxpC 5jy0C C: citing same article (ref.)
Similar structure data	5jwi-d 1xtu-d 5fa6-d 2va8-d 6dew-d 3l4d-d 3bxb-d 6wjf-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#133 - Jan 2011 Nitric Oxide Synthase similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1)

Deposited unit

A: Asp/Glu-specific dipeptidyl-peptidase

B: Asp/Glu-specific dipeptidyl-peptidase

hetero molecules

160 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)	111.810, 114.403, 147.824
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

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Protein , 1 types, 2 molecules AB

#1: Protein	Asp/Glu-specific dipeptidyl-peptidase / Dipeptidyl-peptidase 11 / DPP11 Mass: 79749.352 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porphyromonas endodontalis (bacteria) / Gene: dpp11, PeDPP11 / Production host: Escherichia coli (E. coli) References: UniProt: F8WQK8, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases

#1: Protein

Asp/Glu-specific dipeptidyl-peptidase / Dipeptidyl-peptidase 11 / DPP11

Mass: 79749.352 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Porphyromonas endodontalis (bacteria) / Gene: dpp11, PeDPP11 / Production host:

Escherichia coli (E. coli)
References: UniProt: F8WQK8, Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases

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Non-polymers , 5 types, 427 molecules

#2: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂ / Details: dipeptide
#3: Chemical	ChemComp-ASP / ASPARTIC ACID Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₇NO₄ / Details: dipeptide
#4: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.95 Å³/Da / Density % sol: 58.35 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.12 M Ethylene glycols, 0.1 M Buffer system 3 pH 8.5, 40% v/v Ethylene glycol, 20% w/v PEG 8000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID29 / Wavelength: 1.008 Å

Detector

Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2015

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.008 Å / Relative weight: 1

Reflection

Resolution: 2.2→90.473 Å / Num. obs: 96263 / % possible obs: 99.6 % / Redundancy: 4.7 % / B_iso Wilson estimate: 45.51 Å² / R_sym value: 0.061 / Net I/av σ(I): 9.476 / Net I/σ(I): 14.9

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
2.2-2.32	4.6	0.744	1	1	99.1
2.32-2.46	4.9	0.49	1.6	1	99.9
2.46-2.63	4.8	0.295	2.6	1	99.9
2.63-2.84	4.6	0.178	4.3	1	99.5
2.84-3.11	4.9	0.106	7.2	1	99.9
3.11-3.48	4.7	0.063	11.5	1	99.9
3.48-4.02	4.6	0.041	16.9	1	99.6
4.02-4.92	4.6	0.032	20.5	1	99.7
4.92-6.96	4.5	0.03	21.5	1	99.7
6.96-45.237	4.3	0.028	16.8	1	98.7

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Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX		refinement
PDB_EXTRACT	3.2	data extraction
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→45.237 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.81

	R_factor	Num. reflection	% reflection
R_free	0.2265	4811	5 %
R_work	0.1815	-	-
obs	0.1838	96188	99.53 %

Solvent computation

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

Displacement parameters

B_iso max: 197.48 Å² / B_iso mean: 64.7478 Å² / B_iso min: 19.12 Å²

Refinement step

Cycle: final / Resolution: 2.2→45.237 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10804	0	45	421	11270
B_iso mean	-	-	49.24	53.25	-
Num. residues	-	-	-	-	1398

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	11053
X-RAY DIFFRACTION	f_angle_d	1.141	14976
X-RAY DIFFRACTION	f_chiral_restr	0.046	1593
X-RAY DIFFRACTION	f_plane_restr	0.005	1979
X-RAY DIFFRACTION	f_dihedral_angle_d	14.051	4020

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.2-2.225	0.3552	148	0.2821	2977	3125	99
2.225-2.2512	0.3393	169	0.2736	2949	3118	98
2.2512-2.2786	0.3157	151	0.2712	3004	3155	99
2.2786-2.3075	0.334	150	0.2474	3007	3157	100
2.3075-2.3378	0.3132	184	0.2395	3010	3194	100
2.3378-2.3699	0.2522	169	0.2336	3018	3187	100
2.3699-2.4037	0.2599	154	0.2263	3006	3160	100
2.4037-2.4396	0.3035	171	0.2277	3050	3221	100
2.4396-2.4777	0.3014	156	0.2202	3012	3168	100
2.4777-2.5183	0.3135	157	0.22	3020	3177	100
2.5183-2.5618	0.2875	166	0.2143	3048	3214	100
2.5618-2.6083	0.2675	149	0.2009	3015	3164	100
2.6083-2.6585	0.2563	166	0.201	3047	3213	100
2.6585-2.7127	0.2445	173	0.1997	3011	3184	99
2.7127-2.7717	0.2428	155	0.1897	2981	3136	99
2.7717-2.8362	0.2693	155	0.1919	3039	3194	100
2.8362-2.9071	0.2428	145	0.1921	3078	3223	100
2.9071-2.9857	0.2521	152	0.1937	3043	3195	100
2.9857-3.0735	0.2372	149	0.1989	3056	3205	100
3.0735-3.1727	0.2691	159	0.2117	3060	3219	100
3.1727-3.2861	0.2623	169	0.2142	3048	3217	100
3.2861-3.4176	0.2649	157	0.1965	3055	3212	100
3.4176-3.5731	0.2324	170	0.185	3047	3217	99
3.5731-3.7614	0.2157	131	0.1795	3077	3208	100
3.7614-3.9969	0.2156	189	0.1657	3066	3255	100
3.9969-4.3053	0.1647	147	0.1489	3072	3219	100
4.3053-4.7381	0.1617	167	0.1327	3099	3266	100
4.7381-5.4228	0.1964	152	0.1524	3112	3264	99
5.4228-6.8284	0.2257	184	0.1753	3122	3306	99
6.8284-45.2463	0.1752	167	0.1569	3248	3415	98

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	2.3184	-0.8795	-0.4286	2.1797	0.3815	1.2044	-0.135	-0.455	-0.0875	0.4505	0.004	-0.0249	0.0114	0.1817	0.1077	0.3467	-0.062	-0.0277	0.4064	0.0085	0.2687	13.8793	-20.5638	-12.8541
2	1.3439	-0.3435	-0.4484	1.5262	-0.0256	1.3565	-0.1005	-0.1254	-0.1884	0.243	-0.1036	0.1521	0.1801	-0.0517	0.202	0.309	-0.0423	0.0464	0.3335	-0.0233	0.2855	4.1758	-28.2664	-20.8753
3	2.2895	-0.4756	-1.6386	0.8502	0.5159	1.5311	-0.3004	-0.4052	-0.4163	0.3879	-0.0382	0.2455	0.542	-0.0433	0.3481	0.6058	-0.0832	0.1713	0.5923	0.0702	0.562	-9.4475	-41.6857	-1.5032
4	1.301	-0.0793	-0.0538	2.1394	0.2641	1.9488	0.0171	0.0328	0.2089	-0.0824	-0.1279	0.1161	-0.3826	-0.0845	0.109	0.2738	-0.0026	0.0034	0.2766	-0.0476	0.2617	2.9445	-12.1073	-29.4419
5	2.2191	-1.3466	0.4771	5.5668	0.2966	1.2494	0.2512	0.4153	-0.392	-0.981	-0.3653	1.592	0.0523	-0.2053	0.0448	0.4872	0.0305	-0.3203	0.4729	-0.1289	0.6699	-29.0039	-27.3253	-64.8672
6	2.9002	-0.6895	-0.2867	8.0122	-0.9473	2.1074	-0.0893	-0.2763	0.1229	0.9825	0.008	1.7286	-0.4669	-0.2022	0.0409	0.3953	0.0003	0.098	0.4242	-0.0925	0.6909	-32.8841	-8.2427	-48.505
7	2.1628	0.3304	-0.1457	2.5877	-1.5917	1.2262	0.1063	-0.371	-0.6531	0.1068	0.0289	2.1091	0.2854	-0.3969	-0.3158	0.8753	-0.211	0.5226	0.9217	0.0671	2.3772	-49.7385	-39.1691	-42.7316
8	2.3187	-1.4108	0.4537	5.3244	0.2783	1.2424	0.1428	0.2595	-0.065	-0.5324	-0.1891	0.5804	-0.0311	-0.0329	0.0509	0.295	0.0112	-0.0688	0.3354	-0.0308	0.251	-18.9474	-24.3639	-57.6529
9	2	-8.3191	1.7835	2.0033	3.0921	2.0007	-0.2307	-0.8021	-0.1696	0.8608	-0.0894	0.3773	-0.3791	-0.2808	0.3261	0.2841	-0.0284	0.0837	0.5597	-0.216	0.5587	-0.1369	-22.994	-22.5044
10	5.3149	-9.5117	6.3006	2.0029	-9.67	7.7087	0.0327	-0.0842	-0.5493	-0.2518	0.8152	1.81	0.0984	-1.118	-0.8911	0.3808	0.0415	0.0091	0.4326	0.0009	0.4921	-24.1017	-27.3425	-54.0912

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 21 through 184 )	A	21 - 184
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 185 through 399 )	A	185 - 399
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 400 through 560 )	A	400 - 560
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 561 through 723 )	A	561 - 723
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 21 through 323 )	B	21 - 323
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 324 through 385 )	B	324 - 385
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 386 through 521 )	B	386 - 521
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 522 through 718 )	B	522 - 718
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 1 through 2 )	D	1 - 2
10	X-RAY DIFFRACTION	10	chain 'E' and (resid 1 through 2 )	E	1 - 2

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