+Open data
-Basic information
Entry | Database: PDB / ID: 6yit | ||||||
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Title | Trypsin inhibitor in complex with bovine trypsin | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / Fragment / protease / Serine protease | ||||||
Function / homology | Function and homology information trypsin / serpin family protein binding / serine protease inhibitor complex / digestion / endopeptidase activity / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Badran, M.J. / Heine, A. / Klebe, G. | ||||||
Citation | Journal: To Be Published Title: Trypsin inhibitor in complex with bovine trypsin Authors: Badran, M.J. / 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 | 6yit.cif.gz | 166.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yit.ent.gz | 109.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yit.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/6yit ftp://data.pdbj.org/pub/pdb/validation_reports/yi/6yit | HTTPS FTP |
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-Related structure data
Related structure data | 6yisC 6yiuC 6yivC 6yiwC 6yixC 6yiyC 6yzaC 6yzcC 6zfjC 6zfkC 5mnkS S: Starting model for refinement C: citing same article (ref.) |
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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 on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin |
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-Non-polymers , 5 types, 172 molecules
#2: Chemical | ChemComp-SO4 / | ||
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#3: Chemical | ChemComp-CA / | ||
#4: Chemical | ChemComp-8M2 / [ | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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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: 1.8 Å3/Da / Density % sol: 31.54 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfat, PEG 8000, ethylene glycol, HEPES / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Ambient temp details: liquid nitrogen / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 26, 2019 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→50 Å / Num. obs: 52150 / % possible obs: 0.99 % / Redundancy: 6.5 % / Biso Wilson estimate: 12.95 Å2 / CC1/2: 0.99 / Net I/σ(I): 16.62 |
Reflection shell | Resolution: 1.25→1.33 Å / Num. unique obs: 8335 / CC1/2: 0.84 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5mnk Resolution: 1.25→43.29 Å / SU ML: 0.0938 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 13.8357 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: 16.25 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.25→43.29 Å
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Refine LS restraints |
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LS refinement shell |
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