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Yorodumi- PDB-5rdv: PanDDA analysis group deposition -- Endothiapepsin ground state m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5rdv | ||||||
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Title | PanDDA analysis group deposition -- Endothiapepsin ground state model 52 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / FragMAX / FragMAXapp / fragment screening / inhibition / F2X-Entry | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å | ||||||
Authors | Weiss, M.S. / Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. | ||||||
Citation | Journal: Structure / Year: 2020 Title: F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries for Crystallographic Fragment Screening. Authors: Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5rdv.cif.gz | 77.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5rdv.ent.gz | 59.6 KB | Display | PDB format |
PDBx/mmJSON format | 5rdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5rdv_validation.pdf.gz | 415.3 KB | Display | wwPDB validaton report |
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Full document | 5rdv_full_validation.pdf.gz | 415.3 KB | Display | |
Data in XML | 5rdv_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | 5rdv_validation.cif.gz | 22.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rd/5rdv ftp://data.pdbj.org/pub/pdb/validation_reports/rd/5rdv | HTTPS FTP |
-Group deposition
ID | G_1002147 (88 entries) |
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Title | PanDDA analysis of F2X-Entry vs. Endothiapepsin |
Type | undefined |
Description | PanDDA analysis of F2X-Entry vs. Endothiapepsin, including auto-refined models with ligands placed according to PanDDA-map and automatically refined models necessary to reproduce ground state model |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#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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#2: Water | ChemComp-HOH / |
-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: 35.26 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.827 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 30, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.827 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.08→42.79 Å / Num. obs: 128689 / % possible obs: 96.9 % / Redundancy: 6.618 % / Biso Wilson estimate: 16.597 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.12 / Χ2: 0.975 / Net I/σ(I): 8.21 / Num. measured all: 901669 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.08→42.79 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.85 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.034 / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 56.46 Å2 / Biso mean: 14.051 Å2 / Biso min: 8.7 Å2
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Refinement step | Cycle: final / Resolution: 1.08→42.79 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.077→1.105 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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