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Yorodumi- PDB-7adg: Cocktail experiment G: fragments 216 and 338 at 90 mM concentrati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7adg | ||||||
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Title | Cocktail experiment G: fragments 216 and 338 at 90 mM concentration in complex with Endothiapepsin | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / aspartic protease / monomer | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07946365588 Å | ||||||
Authors | Hassaan, E. / Klebe, G. / Heine, A. / Schiebel, J. / Koester, H. | ||||||
Citation | Journal: To Be Published Title: Comparison of Cocktail Screening in X-Ray Crystallography vs NMR Authors: Hassaan, E. / Klebe, G. / Heine, A. / Schiebel, J. / Koester, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7adg.cif.gz | 248.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7adg.ent.gz | 163.8 KB | Display | PDB format |
PDBx/mmJSON format | 7adg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ad/7adg ftp://data.pdbj.org/pub/pdb/validation_reports/ad/7adg | HTTPS FTP |
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-Related structure data
Related structure data | 5dq4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 43278.664 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, endothiapepsin |
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-Non-polymers , 6 types, 398 molecules
#2: Chemical | ChemComp-483 / | ||||
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#3: Chemical | ChemComp-8NE / [ | ||||
#4: Chemical | ChemComp-GOL / | ||||
#5: Chemical | ChemComp-DMS / #6: Chemical | ChemComp-ACT / | #7: Water | ChemComp-HOH / | |
-Details
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: 1.9 Å3/Da / Density % sol: 35.4 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystals obtained by streak-seeding |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.08→42.7 Å / Num. obs: 138339 / % possible obs: 99.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 8.98695266584 Å2 / CC1/2: 0.998 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.08→1.14 Å / Num. unique obs: 22228 / CC1/2: 0.775 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5DQ4 Resolution: 1.07946365588→26.895082891 Å / SU ML: 0.0724161707854 / Cross valid method: FREE R-VALUE / σ(F): 1.36531898138 / Phase error: 12.6809857329 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.7713797583 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07946365588→26.895082891 Å
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Refine LS restraints |
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LS refinement shell |
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