+Open data
-Basic information
Entry | Database: PDB / ID: 6eoo | ||||||
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Title | DPP8 - Apo, space group 20 | ||||||
Components | Dipeptidyl peptidase 8 | ||||||
Keywords | HYDROLASE / DPP8 | ||||||
Function / homology | Function and homology information dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / aminopeptidase activity / serine-type peptidase activity / immune response / apoptotic process / proteolysis / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 | 6eoo.cif.gz | 500.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6eoo.ent.gz | 407.5 KB | Display | PDB format |
PDBx/mmJSON format | 6eoo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6eoo_validation.pdf.gz | 450.5 KB | Display | wwPDB validaton report |
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Full document | 6eoo_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 6eoo_validation.xml.gz | 81.1 KB | Display | |
Data in CIF | 6eoo_validation.cif.gz | 112.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eo/6eoo ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eoo | HTTPS FTP |
-Related structure data
Related structure data | 6eopC 6eoqC 6eorC 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: 103483.352 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q6V1X1, dipeptidyl-peptidase IV #2: 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: 4.23 Å3/Da / Density % sol: 70.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: Na Citrate 0.46M |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91587 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91587 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.65 Å / Num. obs: 180252 / % possible obs: 99.9 % / Redundancy: 8.52 % / Rsym value: 0.1 / Net I/σ(I): 13.2 |
Reflection shell | Resolution: 2.5→2.66 Å / Redundancy: 8.55 % / Mean I/σ(I) obs: 1.92 / Num. unique obs: 30424 / CC1/2: 0.72 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ORV Resolution: 2.5→44.65 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.929 / SU B: 10.522 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.278 / ESU R Free: 0.222 / 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: 63.734 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→44.65 Å
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Refine LS restraints |
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