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- PDB-7y4f: bacterial DPP4 -

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Basic information

Entry
Database: PDB / ID: 7y4f
Titlebacterial DPP4
ComponentsDipeptidyl peptidase IV
KeywordsHYDROLASE / gut microbiota
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.918 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
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase IV
B: Dipeptidyl peptidase IV
C: Dipeptidyl peptidase IV
D: Dipeptidyl peptidase IV


Theoretical massNumber of molelcules
Total (without water)336,7574
Polymers336,7574
Non-polymers00
Water50,4782802
1
A: Dipeptidyl peptidase IV
C: Dipeptidyl peptidase IV


Theoretical massNumber of molelcules
Total (without water)168,3782
Polymers168,3782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-13 kcal/mol
Surface area53810 Å2
MethodPISA
2
B: Dipeptidyl peptidase IV
D: Dipeptidyl peptidase IV


Theoretical massNumber of molelcules
Total (without water)168,3782
Polymers168,3782
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-12 kcal/mol
Surface area54050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.800, 148.857, 137.125
Angle α, β, γ (deg.)90.000, 104.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dipeptidyl peptidase IV


Mass: 84189.148 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)
Gene: BT_4193 / Production host: Escherichia coli K-12 (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2802 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M BICINE pH 9.0, 10% w/v PEG 20,000 and 3% 6-aminohexanoic acid solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9783 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9783 Å / Relative weight: 1
ReflectionResolution: 1.918→46.364 Å / Num. obs: 283945 / % possible obs: 99.4 % / Redundancy: 3.4 % / CC1/2: 0.984 / Net I/σ(I): 12.6
Reflection shellResolution: 1.92→1.95 Å / Num. unique obs: 3107 / CC1/2: 0.512

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R9N

1r9n


Resolution: 1.918→46.364 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1933 14246 5.04 %
Rwork0.1678 268348 -
obs0.1691 282594 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.21 Å2 / Biso mean: 33.6901 Å2 / Biso min: 15.23 Å2
Refinement stepCycle: final / Resolution: 1.918→46.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23080 0 0 2802 25882
Biso mean---40.8 -
Num. residues----2856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.918-1.93970.33194530.2974834793
1.9397-1.96250.28814490.2776895999
1.9625-1.98640.28094780.2576889099
1.9864-2.01160.26014800.24678924100
2.0116-2.03810.27564850.24028954100
2.0381-2.0660.26124490.2365893999
2.066-2.09550.24484630.21838925100
2.0955-2.12680.2384420.21499079100
2.1268-2.160.25244830.20238922100
2.16-2.19540.2124530.19368965100
2.1954-2.23330.23224800.19158954100
2.2333-2.27390.21075130.18548971100
2.2739-2.31760.22414730.18448910100
2.3176-2.36490.21575020.17768976100
2.3649-2.41630.20554690.17528957100
2.4163-2.47250.23064640.17968976100
2.4725-2.53440.21424620.1832897099
2.5344-2.60290.22084740.17478952100
2.6029-2.67950.21344510.17588997100
2.6795-2.76590.21124840.17599011100
2.7659-2.86480.19784680.17098963100
2.8648-2.97950.20474570.16729012100
2.9795-3.1150.19144990.16298949100
3.115-3.27920.18654950.1619886499
3.2792-3.48460.19154700.15679017100
3.4846-3.75360.1565050.14738960100
3.7536-4.13110.16494860.13649026100
4.1311-4.72840.14184860.122893499
4.7284-5.95530.14894500.1383905499
5.9553-46.3640.17525230.161899199

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