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Yorodumi- PDB-5r21: PanDDA analysis group deposition -- Endothiapepsin in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5r21 | ||||||
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Title | PanDDA analysis group deposition -- Endothiapepsin in complex with fragment F2X-Entry E07, DMSO-free | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.047 Å | ||||||
Authors | Wollenhaupt, J. / Metz, A. / Barthel, T. / Lima, G.M.A. / Heine, A. / Mueller, U. / Klebe, G. / Weiss, M.S. | ||||||
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 | 5r21.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5r21.ent.gz | 163 KB | Display | PDB format |
PDBx/mmJSON format | 5r21.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5r21_validation.pdf.gz | 767.1 KB | Display | wwPDB validaton report |
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Full document | 5r21_full_validation.pdf.gz | 767 KB | Display | |
Data in XML | 5r21_validation.xml.gz | 15.8 KB | Display | |
Data in CIF | 5r21_validation.cif.gz | 24.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/5r21 ftp://data.pdbj.org/pub/pdb/validation_reports/r2/5r21 | HTTPS FTP |
-Group deposition
ID | G_1002120 (81 entries) |
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Title | PanDDA analysis of F2X-Entry Screen vs. Endothiapepsin, DMSO-free soaking |
Type | undefined |
Description | PanDDA analysis of F2X-Entry Screen vs. Endothiapepsin, DMSO-free soaking, 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 / Details: cell Source: (natural) Cryphonectria parasitica (chestnut blight fungus) References: UniProt: P11838, EC: 3.4.23.22 |
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#2: Chemical | ChemComp-R9Y / |
#3: 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: 1.89 Å3/Da / Density % sol: 34.93 % |
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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% PEG4000 |
-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: 1.05→42.63 Å / Num. obs: 149937 / % possible obs: 99.1 % / Redundancy: 6.766 % / Biso Wilson estimate: 17.022 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.072 / Χ2: 1.247 / Net I/σ(I): 10.46 / Num. measured all: 1015175 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.047→42.63 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 18.67 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 56.5 Å2 / Biso mean: 18.9338 Å2 / Biso min: 11.43 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.047→42.63 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15
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