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Yorodumi- PDB-3t7x: Endothiapepsin in complex with an inhibitor based on the Gewald r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t7x | ||||||
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Title | Endothiapepsin in complex with an inhibitor based on the Gewald reaction | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å | ||||||
Authors | Koester, H. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To be Published Title: Endothiapepsin in complex with an inhibitor based on the Gewald reaction Authors: Koester, H. / 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 | 3t7x.cif.gz | 84.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t7x.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 3t7x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t7/3t7x ftp://data.pdbj.org/pub/pdb/validation_reports/t7/3t7x | HTTPS FTP |
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-Related structure data
Related structure data | 3t7qC 1oewS C: citing same article (ref.) S: Starting model for refinement |
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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-4SH / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.85 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 0.1M NH4Ac, 0.1M acetate-buffer, 26% PEG4000, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 289K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Nov 5, 2009 / Details: mirrors |
Radiation | Monochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 1.27→25 Å / Num. all: 84384 / Num. obs: 84384 / % possible obs: 100 % / Redundancy: 3.1 % / Rsym value: 4 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.27→1.29 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 6.1 / Num. unique all: 3480 / Rsym value: 16.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1OEW Resolution: 1.27→21.598 Å / SU ML: 0.12 / Cross valid method: FREE R / σ(F): 1 / Phase error: 14.17 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 63.614 Å2 / ksol: 0.459 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.27→21.598 Å
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Refine LS restraints |
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LS refinement shell |
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