+Open data
-Basic information
Entry | Database: PDB / ID: 6eor | ||||||
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Title | DPP9 - 1G244 | ||||||
Components | Dipeptidyl peptidase 9 | ||||||
Keywords | HYDROLASE / DPP9 | ||||||
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.R. / Huber, R. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Structures and mechanism of dipeptidyl peptidases 8 and 9, important players in cellular homeostasis and cancer. Authors: Ross, B. / Krapp, S. / Augustin, M. / Kierfersauer, R. / Arciniega, M. / Geiss-Friedlander, R. / Huber, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6eor.cif.gz | 652.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eor.ent.gz | 534.5 KB | Display | PDB format |
PDBx/mmJSON format | 6eor.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eor_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6eor_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 6eor_validation.xml.gz | 108.3 KB | Display | |
Data in CIF | 6eor_validation.cif.gz | 147.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/6eor ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eor | HTTPS FTP |
-Related structure data
Related structure data | 6eooC 6eopC 6eoqC 6eosC 6eotC 1orvS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 99213.211 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-9XH / ( #3: Water | ChemComp-HOH / | |
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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: 2.77 Å3/Da / Density % sol: 55.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 10% PEG 8000, 25% Glycerol, 0.16M Calcium Acetate, 0.08M Cacodilate pH 6.25 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99997 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99997 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→43.5 Å / Num. obs: 95096 / % possible obs: 99 % / Redundancy: 4.28 % / Rsym value: 0.16 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.9→3.09 Å / Redundancy: 4.38 % / Mean I/σ(I) obs: 4.98 / Num. unique obs: 16260 / CC1/2: 0.94 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ORV Resolution: 2.9→43.52 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.842 / SU B: 23.591 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.595 Å2
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Refinement step | Cycle: 1 / Resolution: 2.9→43.52 Å
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