+Open data
-Basic information
Entry | Database: PDB / ID: 6scv | ||||||
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Title | Endothiapepsin in complex with ligand 69 | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE / Aspartic Proteinase / Endothiapepsin / Complex with tetrazole / Inhibitor | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Magari, F. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Endothiapepsin in complex with ligand 69 Authors: Magari, F. / Heine, A. / Konstantinidou, M. / Sutanto, F. / Haupenthal, J. / Jumde, R.V. / Unver, M.Y. / Camacho, C.J. / Hirsch, A.K.H. / Doemling, 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 | 6scv.cif.gz | 215.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6scv.ent.gz | 149.3 KB | Display | PDB format |
PDBx/mmJSON format | 6scv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sc/6scv ftp://data.pdbj.org/pub/pdb/validation_reports/sc/6scv | HTTPS FTP |
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-Related structure data
Related structure data | |
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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
#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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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-L7K / [(~{ |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.58 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1 M AMMONIUM ACETATE, 0.1M SODIUM ACETATE, 24-30% PEG 4000 CRYSTAL OBTAINED BY STREAK-SEEDING |
-Data collection
Diffraction | Mean temperature: 113 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.542 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 31, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. obs: 35726 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.999 / Rsym value: 0.038 / Net I/σ(I): 24.79 |
Reflection shell | Resolution: 1.7→1.8 Å / Mean I/σ(I) obs: 6.26 / Num. unique obs: 5629 / CC1/2: 0.947 / Rsym value: 0.224 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: NONE Resolution: 1.7→39.58 Å / SU ML: 0.1262 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.8521
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→39.58 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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