+Open data
-Basic information
Entry | Database: PDB / ID: 5qbr | ||||||
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Title | Crystal structure of Endothiapepsin | ||||||
Components | Endothiapepsin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information 4-hydroxy-3-polyprenylbenzoate decarboxylase / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase activity / ferulate metabolic process / cinnamic acid catabolic process / ubiquinone biosynthetic process / metal ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Cryphonectria parasitica (chestnut blight fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.418 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 | 5qbr.cif.gz | 146.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qbr.ent.gz | 120.7 KB | Display | PDB format |
PDBx/mmJSON format | 5qbr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5qbr_validation.pdf.gz | 699.6 KB | Display | wwPDB validaton report |
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Full document | 5qbr_full_validation.pdf.gz | 699.6 KB | Display | |
Data in XML | 5qbr_validation.xml.gz | 16.6 KB | Display | |
Data in CIF | 5qbr_validation.cif.gz | 26 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/5qbr ftp://data.pdbj.org/pub/pdb/validation_reports/qb/5qbr | HTTPS FTP |
-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
-Protein , 1 types, 1 molecules A
#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, EC: 3.4.23.22 |
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-Non-polymers , 5 types, 341 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | #5: Chemical | ChemComp-DD4 / ( | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.32 % |
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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: 1.42→41.465 Å / Num. obs: 62097 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.26 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Rrim(I) all: 0.097 / Χ2: 1.076 / Net I/σ(I): 9.93 / Num. measured all: 230730 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Resolution: 1.418→41.465 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 21.83 / 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: 52.14 Å2 / Biso mean: 19.0904 Å2 / Biso min: 7.75 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.418→41.465 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: 15
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