+Open data
-Basic information
Entry | Database: PDB / ID: 5qb7 | ||||||
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Title | Crystal structure of Endothiapepsin-FRG075 complex | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.5 Å | ||||||
Authors | Huschmann, F. | ||||||
Citation | Journal: To be published Title: Crystal structure of Endothiapepsin Authors: Huschmann, F.U. / Weiss, M.S. / Mueller, U. / Haustedt, L.O. / Klebe, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qb7.cif.gz | 148.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qb7.ent.gz | 122.6 KB | Display | PDB format |
PDBx/mmJSON format | 5qb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/5qb7 ftp://data.pdbj.org/pub/pdb/validation_reports/qb/5qb7 | HTTPS FTP |
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-Group deposition
ID | G_1002039 (25 entries) |
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Title | Crystal structures of Endothiapepsin complexes |
Type | undefined |
Description | Crystal structures of Endothiapepsin complexes |
-Related structure data
Similar structure data |
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-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 | #4: Chemical | ChemComp-D6A / ( | #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: 2.47 Å3/Da / Density % sol: 50.19 % |
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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, 24-30% PEG 4000; crystals obtained by streak-seeding |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.918 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→42.703 Å / Num. obs: 50671 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.108 / Χ2: 0.894 / Net I/σ(I): 10.3 / Num. measured all: 191704 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Processing
Software |
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Refinement | Method to determine structure: molecular replacement / Resolution: 1.5→42.703 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.01 / 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: 68.15 Å2 / Biso mean: 18.72 Å2 / Biso min: 8.14 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.5→42.703 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7
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