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- PDB-5mb7: Cocktail experiment B: fragments 224 and 236 at 50mM concentration -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mb7 | ||||||
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Title | Cocktail experiment B: fragments 224 and 236 at 50mM concentration | ||||||
![]() | Endothiapepsin![]() | ||||||
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Function / homology | ![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Radeva, N. / Koester, H. / Heine, A. / Klebe, G. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Comparison of cocktail 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.4 KB | Display | ![]() |
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PDB format | ![]() | 149.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5mb6C ![]() 4y5lS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 33813.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() References: UniProt: P11838, ![]() |
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#2: Chemical | ChemComp-GOL / ![]() |
#3: Chemical | ChemComp-4AV / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.23 % |
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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, PEG 4000; crystals obtained by streak-seeding |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Jun 24, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.3→30 Å / Num. obs: 78870 / % possible obs: 99.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.3 |
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4Y5L Resolution: 1.299→18.926 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.48 / 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: 1.299→18.926 Å
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Refine LS restraints |
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LS refinement shell |
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