+Open data
-Basic information
Entry | Database: PDB / ID: 6fid | ||||||
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Title | Bovine trypsin solved by S-SAD on ID30B | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / Benzamidine inhibitor complex / S-SAD | ||||||
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 / SAD / Resolution: 2.2 Å | ||||||
Authors | McCarthy, A.A. / Mueller-Dieckmann, C. | ||||||
Citation | Journal: J Synchrotron Radiat / Year: 2018 Title: ID30B - a versatile beamline for macromolecular crystallography experiments at the ESRF. Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, ...Authors: McCarthy, A.A. / Barrett, R. / Beteva, A. / Caserotto, H. / Dobias, F. / Felisaz, F. / Giraud, T. / Guijarro, M. / Janocha, R. / Khadrouche, A. / Lentini, M. / Leonard, G.A. / Lopez Marrero, M. / Malbet-Monaco, S. / McSweeney, S. / Nurizzo, D. / Papp, G. / Rossi, C. / Sinoir, J. / Sorez, C. / Surr, J. / Svensson, O. / Zander, U. / Cipriani, F. / Theveneau, P. / Mueller-Dieckmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fid.cif.gz | 56.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fid.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fid.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fi/6fid ftp://data.pdbj.org/pub/pdb/validation_reports/fi/6fid | HTTPS FTP |
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-Related structure data
Related structure data | 6fj2C 6fj4C 6fj6C 6fj8C 6fj9C C: citing same article (ref.) |
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Similar structure data | |
Experimental dataset #1 | Data reference: 10.15785/SBGRID/541 / Data set type: diffraction image 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 genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Production host: Bos taurus (cattle) / References: UniProt: P00760, trypsin | ||
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#2: Chemical | ChemComp-CA / | ||
#3: Chemical | ChemComp-BEN / | ||
#4: Chemical | #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: 2.87 Å3/Da / Density % sol: 57.15 % / Description: Long rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 25% PEG 8000, 0.2 M ammonium sulfate and 100mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 2.066 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 15, 2017 / Details: Be CRL/Si Elliptical mirror |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 2.066 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 13845 / % possible obs: 97.2 % / Redundancy: 11.8 % / Biso Wilson estimate: 15.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.024 / Rrim(I) all: 0.118 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 10.4 / Num. unique obs: 1057 / CC1/2: 0.98 / Rpim(I) all: 0.074 / Rrim(I) all: 0.275 / % possible all: 85.8 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.2→47.18 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.272 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.066 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→47.18 Å
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