+Open data
-Basic information
Entry | Database: PDB / ID: 7a3f | ||||||
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Title | Crystal structure of apo DPP9 | ||||||
Components | Dipeptidyl peptidase 9 | ||||||
Keywords | HYDROLASE / DPP9 / Protease | ||||||
Function / homology | Function and homology information dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding ...dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Ross, B.H. / Huber, R. | ||||||
Citation | Journal: To Be Published Title: Discovery and Development of 4-Oxo-beta-Lactams as Novel Inhibitors of Dipeptidyl Peptidases 8 and 9 Authors: Fehr, L. / Carvalho, L.A.R. / Ross, B.H. / Lum, K. / Vieira, A.C. / Kiefersauer, R. / Geiss-Friedlander, R. / Kaiser, M. / Rodrigues, T. / Lucas, S.D. / Cravatt, B.F. / Huber, R. / Moreira, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7a3f.cif.gz | 643.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7a3f.ent.gz | 516.9 KB | Display | PDB format |
PDBx/mmJSON format | 7a3f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7a3f_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7a3f_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7a3f_validation.xml.gz | 103.2 KB | Display | |
Data in CIF | 7a3f_validation.cif.gz | 140.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/7a3f ftp://data.pdbj.org/pub/pdb/validation_reports/a3/7a3f | HTTPS FTP |
-Related structure data
Related structure data | 7a3iC 7a3kC 6eorS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 102627.156 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV #2: Chemical | ChemComp-PO4 / #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.08 M Na-Cacodilate pH 5.25, 0.16 M Ca-Acetate, 30 % Glycerol, 10 % PEG 8K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 28, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.9→46.89 Å / Num. obs: 92941 / % possible obs: 98.4 % / Redundancy: 2.235 % / Biso Wilson estimate: 50.051 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.115 / Χ2: 0.946 / Net I/σ(I): 7.24 / Num. measured all: 207713 / Scaling rejects: 330 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EOR Resolution: 2.9→46.89 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.87 / SU B: 25.629 / SU ML: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 142.73 Å2 / Biso mean: 59.125 Å2 / Biso min: 9.88 Å2
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Refinement step | Cycle: final / Resolution: 2.9→46.89 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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