+Open data
-Basic information
Entry | Database: PDB / ID: 6yix | ||||||
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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 cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 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 | 6yix.cif.gz | 163.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6yix.ent.gz | 107.5 KB | Display | PDB format |
PDBx/mmJSON format | 6yix.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yix_validation.pdf.gz | 960.6 KB | Display | wwPDB validaton report |
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Full document | 6yix_full_validation.pdf.gz | 960.5 KB | Display | |
Data in XML | 6yix_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 6yix_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yi/6yix ftp://data.pdbj.org/pub/pdb/validation_reports/yi/6yix | HTTPS FTP |
-Related structure data
Related structure data | 6yisC 6yitC 6yiuC 6yivC 6yiwC 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
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: ...Details: IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVSAAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLNSRVASISLPTSCASAGTQCLISGWGNTKSSGTSYPDVLKCLKAPILSDSSCKSAYPGQITSNMFCAGYLEGGKDSCQGDSGGPVVCSGKLQGIVSWGSGCAQKNKPGVYTKVCNYVSWIKQTIASN Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-8M2 / [ | #4: Chemical | ChemComp-DMS / #5: 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: 2.04 Å3/Da / Density % sol: 39.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: ammonium sulfat, PEG8000, 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: Jun 29, 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: 1.31→50 Å / Num. obs: 50997 / % possible obs: 98.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 11.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 18.98 |
Reflection shell | Resolution: 1.31→1.39 Å / Redundancy: 4.6 % / Num. unique obs: 8098 / CC1/2: 0.841 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MNK Resolution: 1.31→42.13 Å / SU ML: 0.1189 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.4284
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.31→42.13 Å
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Refine LS restraints |
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LS refinement shell |
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