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- PDB-7y4g: sit-bound btDPP4 -

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Basic information

Entry
Database: PDB / ID: 7y4g
Titlesit-bound btDPP4
ComponentsbtDPP4
KeywordsHYDROLASE/INHIBITOR / gut microbiota / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homologyChem-715
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsHang, J. / Jiang, C. / Wang, K. / Zhang, Z. / Guo, F. / Liu, J. / Wang, G. / Lei, X. / Gonzalez, F. / Qiao, J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82071658 China
CitationJournal: 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. / ...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. / Pang, Y. / Wang, G. / Gonzalez, F.J. / Lei, X. / Qiao, J. / Jiang, C.
History
DepositionJun 14, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title
Revision 1.2Aug 30, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: btDPP4
B: btDPP4
C: btDPP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,2236
Polymers246,0013
Non-polymers1,2223
Water21,6361201
1
A: btDPP4
hetero molecules

A: btDPP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,8154
Polymers164,0012
Non-polymers8152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area5310 Å2
ΔGint-6 kcal/mol
Surface area53460 Å2
MethodPISA
2
B: btDPP4
C: btDPP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,8154
Polymers164,0012
Non-polymers8152
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-4 kcal/mol
Surface area53780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.298, 110.991, 134.392
Angle α, β, γ (deg.)90.00, 91.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein btDPP4


Mass: 82000.320 Da / Num. of mol.: 3
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 (E. coli)
#2: Chemical ChemComp-715 / (2R)-4-OXO-4-[3-(TRIFLUOROMETHYL)-5,6-DIHYDRO[1,2,4]TRIAZOLO[4,3-A]PYRAZIN-7(8H)-YL]-1-(2,4,5-TRIFLUOROPHENYL)BUTAN-2-A MINE / Sitagliptin


Mass: 407.314 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H15F6N5O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.55 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH6.0, 14% PEG 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jan 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.89→69.76 Å / Num. obs: 143666 / % possible obs: 92.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 11.7
Reflection shellResolution: 1.89→1.89 Å / Rmerge(I) obs: 0.556 / Num. unique obs: 3243

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R9N

1r9n


Resolution: 1.97→44.79 Å / SU ML: 0.27 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 34.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2627 1984 1.38 %
Rwork0.2232 --
obs0.2238 143666 84.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.97→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17421 0 0 1201 18622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0317871
X-RAY DIFFRACTIONf_angle_d3.51524195
X-RAY DIFFRACTIONf_dihedral_angle_d12.2152406
X-RAY DIFFRACTIONf_chiral_restr0.1892526
X-RAY DIFFRACTIONf_plane_restr0.0273129
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.3658540.31683779X-RAY DIFFRACTION32
2.02-2.080.3574870.30535722X-RAY DIFFRACTION48
2.08-2.140.3108920.29737427X-RAY DIFFRACTION62
2.14-2.210.35271340.28029130X-RAY DIFFRACTION77
2.21-2.290.34441320.271910274X-RAY DIFFRACTION86
2.29-2.380.30941640.266211074X-RAY DIFFRACTION93
2.38-2.490.3021540.255611488X-RAY DIFFRACTION96
2.49-2.620.29371600.246611740X-RAY DIFFRACTION98
2.62-2.780.27651700.243711806X-RAY DIFFRACTION99
2.78-30.27351680.227111948X-RAY DIFFRACTION100
3-3.30.26761740.207311903X-RAY DIFFRACTION100
3.3-3.780.22331640.194811926X-RAY DIFFRACTION99
3.78-4.760.19351660.171411893X-RAY DIFFRACTION99
4.76-44.790.24431650.207211572X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.13130.18990.00581.1869-0.1880.53720.0904-0.11570.09710.1459-0.07560.3934-0.0237-0.11940.00010.1599-0.01340.0360.1995-0.05260.205255.05544.726.7734
21.2328-0.32420.03441.48880.18710.75370.08630.05770.2332-0.1960.0489-0.49870.01680.2398-0.09080.22510.03040.04790.2373-0.03850.263656.07514.5849-50.1064
31.2571-0.5224-0.01321.9205-0.18290.74020.0138-0.2422-0.25150.21220.17990.72380.057-0.166-0.09920.2274-0.01090.06090.32290.1270.39020.66934.6928-39.023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 22 through 801)
2X-RAY DIFFRACTION2(chain 'B' and resid 22 through 801)
3X-RAY DIFFRACTION3(chain 'C' and resid 22 through 801)

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