PDB-8hay: d4-bound btDPP4

ID or keywords:

Entry

Database: PDB / ID: 8hay

Title

d4-bound btDPP4

Components

btDPP4

Keywords

HYDROLASE/INHIBITOR / peptidase / gut microbiota / isozyme / secreted / inhibitor / HYDROLASE / HYDROLASE-INHIBITOR complex

Function / homology

Chem-KYL

Function and homology information

Biological species

Bacteroides thetaiotaomicron (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.74 Å

Authors

Hang, J. / Jiang, C. / Wang, K. / Zhang, Z. / Guo, F. / Liu, J. / Wang, G. / Lei, X. / Gonzalez, F. / Qiao, J.

Funding support

China, 1items

Citation

Journal: Science / Year: 2023
Title: Microbial-host-isozyme analyses reveal microbial DPP4 as a potential antidiabetic target.
Authors: Wang, K. / Zhang, Z. / Hang, J. / Liu, J. / Guo, F. / Ding, Y. / Li, M. / Nie, Q. / Lin, J. / Zhuo, Y. / Sun, L. / Luo, X. / Zhong, Q. / Ye, C. / Yun, C. / Zhang, Y. / Wang, J. / Bao, R. / ...

History

Deposition	Oct 27, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 26, 2023	Provider: repository / Type: Initial release
Revision 1.1	Aug 30, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	8hay.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb8hay.ent.gz	939.1 KB	Display	PDB format
PDBx/mmJSON format	8hay.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8hay_validation.pdf.gz	1.6 MB	Display	wwPDB validaton report
Full document	8hay_full_validation.pdf.gz	1.6 MB	Display
Data in XML	8hay_validation.xml.gz	99.8 KB	Display
Data in CIF	8hay_validation.cif.gz	137.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ha/8hay ftp://data.pdbj.org/pub/pdb/validation_reports/ha/8hay	HTTPS FTP

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Related structure data

Related structure data	7y4fC 7y4gC 1r9nS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: btDPP4

B: btDPP4

C: btDPP4

D: btDPP4

hetero molecules

329 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: btDPP4

C: btDPP4

hetero molecules

defined by author&software
165 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: btDPP4

D: btDPP4

hetero molecules

defined by author&software
164 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	96.106, 149.411, 137.898
Angle α, β, γ (deg.)	90.00, 103.74, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	btDPP4 Mass: 81872.188 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: NCBI accession code: WP_022302284.1 Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria) Production host: Escherichia coli K-12 (bacteria)
#2: Chemical	ChemComp-KYL / (1~{R})-1-[[4-[5-[[(1~{R})-6,7-dimethoxy-2-methyl-3,4-dihydro-1~{H}-isoquinolin-1-yl]methyl]-2-methoxy-phenoxy]phenyl]methyl]-6,7-dimethoxy-2-methyl-3,4-dihydro-1~{H}-isoquinoline Mass: 638.792 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃₉H₄₆N₂O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 304 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	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: 2.94 Å³/Da / Density % sol: 58.12 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 8.35, 12% PEG 3,350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 11, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9792 Å / Relative weight: 1
Reflection	Resolution: 2.74→36.94 Å / Num. obs: 95310 / % possible obs: 96.1 % / Redundancy: 3.5 % / CC_1/2: 0.984 / Net I/σ(I): 7.55
Reflection shell	Resolution: 2.74→2.79 Å / Num. unique obs: 4869 / CC_1/2: 0.615

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Processing

Software

Name	Version	Classification
PHENIX	1.19.1	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1R9N

1r9n

Resolution: 2.74→36.94 Å / Cross valid method: NONE

	R_factor	Num. reflection	% reflection
R_work	0.1985	-	-
R_free	-	9491	-
obs	-	95306	96.1 %

Refinement step

Cycle: LAST / Resolution: 2.74→36.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	23080	0	141	304	23525

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	23828
X-RAY DIFFRACTION	f_angle_d	1.066	32254
X-RAY DIFFRACTION	f_dihedral_angle_d	16.94	8831
X-RAY DIFFRACTION	f_chiral_restr	0.059	3372
X-RAY DIFFRACTION	f_plane_restr	0.009	4164

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 (%)
2.74-2.81	0.3374	140	0.2795	6562	X-RAY DIFFRACTION	95
2.81-2.88	0.2928	146	0.2581	6843	X-RAY DIFFRACTION	99
2.88-2.97	0.2704	148	0.2458	6872	X-RAY DIFFRACTION	99
2.97-3.07	0.2388	147	0.2391	6874	X-RAY DIFFRACTION	99
3.07-3.18	0.2987	148	0.2525	6893	X-RAY DIFFRACTION	100
3.18-3.3	0.2352	147	0.2362	6890	X-RAY DIFFRACTION	100
3.3-3.45	0.2062	147	0.2061	6903	X-RAY DIFFRACTION	100
3.45-3.61	0.225	127	0.2127	5924	X-RAY DIFFRACTION	95
3.65-3.86	0.3101	102	0.2964	4778	X-RAY DIFFRACTION	75
3.86-4.16	0.173	148	0.1635	6897	X-RAY DIFFRACTION	100
4.16-4.58	0.1506	149	0.1311	6959	X-RAY DIFFRACTION	100
4.58-5.24	0.1089	147	0.1226	6898	X-RAY DIFFRACTION	100
5.24-6.59	0.1405	150	0.1492	6980	X-RAY DIFFRACTION	100
6.59-37.55	0.1504	151	0.1404	7031	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	0.0861	-0.0724	0.1163	0.0741	-0.1902	0.4607	-0.0762	-0.1788	0.1188	0.0879	-0.0124	0.0539	-0.321	0.0205	0.0359	0.4855	0.0387	-0.0135	0.3886	-0.0437	0.3914	1.3923	13.3858	28.1406
2	0.3836	0.1576	0.0454	0.4665	0.0337	0.8731	0.0525	-0.1886	0.0367	-0.0125	-0.0693	-0.0769	-0.0876	-0.1351	0.003	0.3009	0.0218	0.0202	0.4413	0.0206	0.3746	1.7576	-3.6882	35.7047
3	0.4563	-0.0153	-0.0224	0.3503	-0.0334	0.1635	0.0576	-0.044	-0.0792	0.0241	-0.0333	0.0757	-0.0126	-0.1305	-0.015	0.263	-0.0212	0.0153	0.3499	0.002	0.2799	-7.1454	-13.2533	20.7822
4	1.2122	-0.1573	-0.251	0.3852	-0.0547	0.4792	-0.0298	0.0919	0.1486	-0.0097	0.032	-0.0012	-0.0761	-0.1191	-0.0174	0.2595	0.001	-0.0125	0.2701	-0.0094	0.269	-0.8622	4.5343	0.0617
5	0.2123	0.1622	0.0612	0.139	0.0897	0.3265	-0.0829	-0.024	0.0083	-0.1281	-0.0395	-0.0009	-0.3325	0.0453	0.0825	0.5216	-0.0473	0.0024	0.366	-0.022	0.4147	-60.9947	15.0599	39.066
6	0.4399	0.0783	-0.1311	0.1876	0.1514	0.7105	-0.0028	-0.065	-0.0164	-0.0153	0.0192	-0.07	0.0099	0.1105	-0.0257	0.2825	-0.0211	0.0079	0.3436	-0.0217	0.3058	-61.0875	-7.1396	45.7996
7	0.6135	0.0461	-0.2765	0.7461	-0.1518	0.6611	0.0621	0.0258	0.0775	-0.0075	-0.0712	-0.0317	-0.1795	0.2785	0.0002	0.3949	-0.094	-0.0031	0.5273	-0.0322	0.4096	-41.9848	10.5261	53.9494
8	0.7323	-0.0205	-0.2015	0.3241	0.1106	0.555	-0.0036	-0.246	0.1634	0.024	0.0513	-0.0043	-0.1754	0.1149	-0.0371	0.3526	-0.0404	-0.0112	0.4062	-0.0243	0.3538	-65.0959	13.9022	74.972
9	0.0395	-0.1677	0.067	0.7514	-0.295	0.1	-0.0013	0.0907	-0.0832	-0.1687	0.0926	0.1751	0.1495	-0.1405	-0.0558	0.4284	-0.0155	0.0026	0.3747	-0.0527	0.4301	44.4267	-35.2404	-20.198
10	0.4727	-0.4366	-0.2309	0.4079	0.1353	0.2824	-0.015	0.0156	-0.1457	0.0672	-0.0473	0.0845	0.0521	0.014	0.0573	0.3016	0.0168	0.0062	0.2203	-0.0087	0.357	41.3167	-35.6815	3.2426
11	0.3656	0.0939	-0.0044	0.862	-0.0103	0.5746	-0.0232	-0.0689	-0.0683	-0.015	0.0514	-0.1235	0.0632	0.1373	-0.0333	0.2364	0.0268	-0.0047	0.2868	-0.0181	0.3469	63.8059	-25.3118	2.1171
12	0.6638	-0.0546	0.0064	0.1414	-0.047	0.4864	-0.013	0.0862	0.0023	-0.0586	0.0157	-0.0395	-0.0456	-0.046	-0.0151	0.2566	-0.018	0.0066	0.2286	-0.0146	0.2786	43.8891	-3.9199	-9.0494
13	0.8214	0.1177	-0.2426	0.2026	0.1323	0.4864	-0.0203	0.003	-0.2482	0.0623	-0.0481	-0.0101	0.1746	-0.1613	0.0524	0.3946	-0.073	-0.0107	0.4407	0.0321	0.3927	-109.0091	-20.7866	78.9345
14	0.6414	0.1657	0.0085	0.2947	0.057	0.7579	0.0128	-0.0819	0.0783	0.0471	-0.0223	0.0541	-0.0366	-0.1891	0.0156	0.298	0.0106	-0.0182	0.4162	0.0091	0.3054	-107.7365	7.5146	81.3979

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 23 through 118 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 119 through 208 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 209 through 379 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 380 through 736 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 23 through 118 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 119 through 314 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 315 through 481 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 482 through 736 )
9	X-RAY DIFFRACTION	9	chain 'C' and (resid 23 through 91 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 92 through 265 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 266 through 442 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 443 through 736 )
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 23 through 379 )
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 380 through 736 )

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