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Yorodumi- PDB-5mb5: Cocktail experiment C: fragments 103 and 171 in complex with Endo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mb5 | ||||||
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Title | Cocktail experiment C: fragments 103 and 171 in complex with Endothiapepsin | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / fragment screening / inhibition | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å | ||||||
Authors | Radeva, N. / Heine, A. / Klebe, G. | ||||||
Funding support | Germany, 1items
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Citation | Journal: To Be Published Title: Comparison of cocktails versus single soaking experiments Authors: Radeva, N. / Heine, A. / Klebe, G. #1: Journal: J. Med. Chem. / Year: 2016 Title: Experimental Active-Site Mapping by Fragments: Hot Spots Remote from the Catalytic Center of Endothiapepsin. Authors: Radeva, N. / Krimmer, S.G. / Stieler, M. / Fu, K. / Wang, X. / Ehrmann, F.R. / Metz, A. / Huschmann, F.U. / Weiss, M.S. / Mueller, U. / Schiebel, J. / Heine, A. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mb5.cif.gz | 198.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mb5.ent.gz | 160.2 KB | Display | PDB format |
PDBx/mmJSON format | 5mb5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mb5_validation.pdf.gz | 314 KB | Display | wwPDB validaton report |
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Full document | 5mb5_full_validation.pdf.gz | 314.1 KB | Display | |
Data in XML | 5mb5_validation.xml.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/5mb5 ftp://data.pdbj.org/pub/pdb/validation_reports/mb/5mb5 | HTTPS FTP |
-Related structure data
Related structure data | 5mb3C 4y5lS 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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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, 414 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-ACT / | #5: Chemical | ChemComp-46P / | #6: 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: 1.9 Å3/Da / Density % sol: 35.12 % |
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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; 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: 0.91841 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 0.98→42.7 Å / Num. obs: 179855 / % possible obs: 97.4 % / Redundancy: 3.8 % / Rsym value: 0.066 / Net I/σ(I): 10.23 |
Reflection shell | Resolution: 0.98→1.04 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.19 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4Y5L Resolution: 0.98→36.483 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.26 / 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: 0.98→36.483 Å
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Refine LS restraints |
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LS refinement shell |
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