+Open data
-Basic information
Entry | Database: PDB / ID: 6qzv | ||||||
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Title | DPP9 bound to a dipeptide (MP) from the N-terminus of BRCA2 | ||||||
Components |
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Keywords | HYDROLASE / DPP8 / DPP9 / BRCA2 / dipeptide | ||||||
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: 3 Å | ||||||
Authors | Ross, B. / Geiss-Friedlander, R. / Huber, R. | ||||||
Citation | Journal: Biorxiv / Year: 2020 Title: Dipeptidyl peptidase 9 triggers BRCA2 degradation by the N-degron pathway to promote DNA-damage repair Authors: Silva-Garcia, M. / Bolgi, O. / Ross, B. / Pilla, E. / Kari, V. / Killisch, M. / Stark, N. / Lenz, C. / Spitzner, M. / Gorrell, M.D. / Grade, M. / Urlaub, H. / Dobbelstein, M. / Huber, R. / Geiss-Friedlander, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qzv.cif.gz | 650.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qzv.ent.gz | 525.2 KB | Display | PDB format |
PDBx/mmJSON format | 6qzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qz/6qzv ftp://data.pdbj.org/pub/pdb/validation_reports/qz/6qzv | HTTPS FTP |
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-Related structure data
Related structure data | 6qzwC 6eoqS 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: Protein/peptide | Mass: 246.326 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) #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: 2.68 Å3/Da / Density % sol: 54.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 Details: 20 mg/ml of protein, 10% PEG 8000, 25% glycerol, 0.16 M calcium acetate, 0.08 M cacodilate pH 6.25. Drops are set in a 1:1 ratio. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00002 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00002 Å / Relative weight: 1 |
Reflection | Resolution: 3→43.47 Å / Num. obs: 76534 / % possible obs: 87.8 % / Redundancy: 2.65 % / CC1/2: 0.98 / Rmerge(I) obs: 0.13 / Net I/σ(I): 5.9 |
Reflection shell | Resolution: 3→3.19 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3 / Num. unique obs: 13092 / CC1/2: 0.93 / % possible all: 88.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EOQ Resolution: 3→43.47 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.828 / SU B: 29.275 / SU ML: 0.533 / Cross valid method: THROUGHOUT / ESU R Free: 0.662 / 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: 25.557 Å2
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Refinement step | Cycle: 1 / Resolution: 3→43.47 Å
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