+Open data
-Basic information
Entry | Database: PDB / ID: 6hp8 | ||||||
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Title | Crystal structure of DPP8 in complex with Val-BoroPro | ||||||
Components | Dipeptidyl peptidase 8 | ||||||
Keywords | HYDROLASE / Val-BoroPro / DPP8 / Protease | ||||||
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 / Resolution: 2.5 Å | ||||||
Authors | Ross, B.H. / Huber, R. | ||||||
Citation | Journal: Thesis / Year: 2019 Title: Improvement of Protein Crystal Diffraction Using Post-Crystallization Methods: Infrared Laser Radiation Controls Crystal Order Authors: Ross, B.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hp8.cif.gz | 521.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hp8.ent.gz | 433.7 KB | Display | PDB format |
PDBx/mmJSON format | 6hp8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hp8_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6hp8_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6hp8_validation.xml.gz | 89.3 KB | Display | |
Data in CIF | 6hp8_validation.cif.gz | 124.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hp/6hp8 ftp://data.pdbj.org/pub/pdb/validation_reports/hp/6hp8 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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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: Chemical | #3: Chemical | #4: Chemical | ChemComp-GOL / #5: 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: 4.22 Å3/Da / Density % sol: 70.82 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 6.75 / Details: 0.46 M Na-citrate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99992 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→44.62 Å / Num. obs: 179844 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rrim(I) all: 0.145 / Net I/σ(I): 15.64 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 8.4 % / Rrim(I) all: 1.56 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Resolution: 2.5→44.62 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 7.978 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.205 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.577 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→44.62 Å
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Refine LS restraints |
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