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Open data
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Basic information
Entry | Database: PDB / ID: 7qlu | ||||||||||||
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Title | Endothiapepsin apo at 100K | ||||||||||||
![]() | Endothiapepsin | ||||||||||||
![]() | HYDROLASE / Endopeptidase | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Huang, C.Y. / Aumonier, S. / Wang, M. | ||||||||||||
Funding support | European Union, 3items
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![]() | ![]() Title: Probing ligand binding of endothiapepsin by `temperature-resolved' macromolecular crystallography. Authors: Huang, C.Y. / Aumonier, S. / Engilberge, S. / Eris, D. / Smith, K.M.L. / Leonarski, F. / Wojdyla, J.A. / Beale, J.H. / Buntschu, D. / Pauluhn, A. / Sharpe, M.E. / Metz, A. / Olieric, V. / 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 | ![]() | 110.6 KB | Display | ![]() |
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PDB format | ![]() | 64.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7qltC ![]() 7qlvC ![]() 7qlwC ![]() 7qlxC ![]() 7qlyC ![]() 7qlzC ![]() 7qm0C ![]() 7qm1C ![]() 7qm3C ![]() 7qm4C ![]() 7qm5C ![]() 7qm6C ![]() 7qm7C ![]() 7qm8C ![]() 7qm9C ![]() 7qmaC ![]() 7qmbC ![]() 7qmcC ![]() 7qmdC ![]() 7qmeC ![]() 7qmfC ![]() 7qmgC ![]() 7qmhC ![]() 7qmiC ![]() 7qmjC ![]() 7qmkC ![]() 7qmlC ![]() 7qmmC ![]() 7qmnC ![]() 7qmoC ![]() 7qmpC ![]() 7qmqC ![]() 7qmrC ![]() 7qmsC ![]() 7qmtC ![]() 7qmuC ![]() 7qmvC ![]() 7qmwC ![]() 7qmxC ![]() 7qmyC ![]() 7qmzC ![]() 7qn0C ![]() 7qn1C ![]() 7qn2C ![]() 7qn3C ![]() 7qn4C ![]() 6rsvS C: citing same article ( S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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) ![]() References: UniProt: P11838, endothiapepsin |
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#2: Chemical | ChemComp-PG5 / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M ammonium acetate, 0.1 M sodium acetate pH 4.6, and 26 - 30% (v/v) PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 8, 2021 |
Radiation | Monochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.41→35.13 Å / Num. obs: 60448 / % possible obs: 96.2 % / Redundancy: 6.77 % / Biso Wilson estimate: 17.15 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.08 / Net I/σ(I): 15.48 |
Reflection shell | Resolution: 1.41→1.46 Å / Redundancy: 6.63 % / Mean I/σ(I) obs: 1.34 / Num. unique obs: 5856 / CC1/2: 0.73 / Rrim(I) all: 1.55 / % possible all: 93.26 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6RSV Resolution: 1.41→35.13 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.943 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 20.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.41→35.13 Å
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Refine LS restraints |
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LS refinement shell |
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