+Open data
-Basic information
Entry | Database: PDB / ID: 4y3y | |||||||||
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Title | Endothiapepsin in complex with fragment B42 | |||||||||
Components | Endothiapepsin | |||||||||
Keywords | HYDROLASE / fragment screening / aspartic protease inhibition | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.346 Å | |||||||||
Authors | Huschmann, F.U. / Linnik, J. / Weiss, M.S. / Mueller, U. | |||||||||
Funding support | Germany, 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2016 Title: Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library. Authors: Huschmann, F.U. / Linnik, J. / Sparta, K. / Uhlein, M. / Wang, X. / Metz, A. / Schiebel, J. / Heine, A. / Klebe, G. / Weiss, M.S. / Mueller, U. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y3y.cif.gz | 200.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y3y.ent.gz | 162.2 KB | Display | PDB format |
PDBx/mmJSON format | 4y3y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4y3y_validation.pdf.gz | 453.1 KB | Display | wwPDB validaton report |
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Full document | 4y3y_full_validation.pdf.gz | 453 KB | Display | |
Data in XML | 4y3y_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 4y3y_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y3/4y3y ftp://data.pdbj.org/pub/pdb/validation_reports/y3/4y3y | HTTPS FTP |
-Related structure data
Related structure data | 4y38C 4y3jC 4y48C 4y4dC 4y4gC 4y4jC 4ze6C 4zeaC 3pcwS C: citing same article (ref.) 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: 33813.855 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 , 5 types, 319 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-DMS / #5: Chemical | ChemComp-DCL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.19 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.346→42.793 Å / Num. obs: 70867 / % possible obs: 99 % / Redundancy: 3.7 % / Rsym value: 0.055 / Net I/σ(I): 18.66 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 3.46 % / Rmerge(I) obs: 0.55 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3PCW Resolution: 1.346→34.728 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 12.67 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.346→34.728 Å
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Refine LS restraints |
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LS refinement shell |
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