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- PDB-7bky: Endothiapepsin structure obtained at 298K with fragment BTB09871 ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7bky | ||||||
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Title | Endothiapepsin structure obtained at 298K with fragment BTB09871 bound from a dataset collected with JUNGFRAU detector | ||||||
![]() | Endothiapepsin | ||||||
![]() | HYDROLASE / FBDD / room temperature / JUNGFRAU | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Engilberge, S. / Huang, C.-Y. / Leonarski, F. / Wojdyla, J.A. / Marsh, M. / Olieric, V. / Wang, M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Endothiapepsin structure obtained at 298K with fragment BTB09871 bound from a dataset collected with JUNGFRAU detector Authors: Engilberge, S. / Huang, C.-Y. / Smith, K.M.L. / Eris, D. / Wojdyla, J.A. / Olieric, V. / Leonarski, F. / Sharpe, M. / Wang, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146 KB | Display | ![]() |
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PDB format | ![]() | 113.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 843.2 KB | Display | ![]() |
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Full document | ![]() | 843.4 KB | Display | |
Data in XML | ![]() | 15.9 KB | Display | |
Data in CIF | ![]() | 23.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6rsvS S: Starting model for refinement |
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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, endothiapepsin | ||||||
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#2: Chemical | ChemComp-U1E / ~{ | ||||||
#3: Chemical | ChemComp-DMS / #4: Chemical | ChemComp-1PE / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 100 mM ammonium acetate, 100 mM sodium acetate pH 4.6 and 26 to 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI JUNGFRAU 4M / Detector: PIXEL / Date: Oct 24, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→43.18 Å / Num. obs: 26345 / % possible obs: 98.82 % / Redundancy: 6.8 % / CC1/2: 0.989 / Rpim(I) all: 0.1072 / Net I/σ(I): 5.62 |
Reflection shell | Resolution: 1.9→1.96 Å / Mean I/σ(I) obs: 0.82 / Num. unique obs: 2556 / CC1/2: 0.353 / Rpim(I) all: 0.6821 |
-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: 6RSV Resolution: 1.9→43.18 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.55 / 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: 97.41 Å2 / Biso mean: 29.6402 Å2 / Biso min: 13.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.9→43.18 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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Refinement TLS params. | Method: refined / Origin x: 3.843 Å / Origin y: 0.6379 Å / Origin z: 5.4864 Å
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Refinement TLS group |
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