+Open data
-Basic information
Entry | Database: PDB / ID: 6swv | ||||||
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Title | Trypsin fast data collection | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE | ||||||
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: 1.432 Å | ||||||
Authors | von Stetten, D. / Mueller-Dieckmann, C. | ||||||
Citation | Journal: J.Synchrotron Radiat. / Year: 2020 Title: ID30A-3 (MASSIF-3) - a beamline for macromolecular crystallography at the ESRF with a small intense beam. Authors: von Stetten, D. / Carpentier, P. / Flot, D. / Beteva, A. / Caserotto, H. / Dobias, F. / Guijarro, M. / Giraud, T. / Lentini, M. / McSweeney, S. / Royant, A. / Petitdemange, S. / Sinoir, J. / ...Authors: von Stetten, D. / Carpentier, P. / Flot, D. / Beteva, A. / Caserotto, H. / Dobias, F. / Guijarro, M. / Giraud, T. / Lentini, M. / McSweeney, S. / Royant, A. / Petitdemange, S. / Sinoir, J. / Surr, J. / Svensson, O. / Theveneau, P. / Leonard, G.A. / 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 | 6swv.cif.gz | 65.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6swv.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6swv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sw/6swv ftp://data.pdbj.org/pub/pdb/validation_reports/sw/6swv | HTTPS FTP |
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-Related structure data
Related structure data | 6y8gC 3atiS 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: 25806.197 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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#2: Chemical | ChemComp-CA / | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-BEN / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 15 mg/ml protein, 100 mM benzamidine, 25% PEG 8000, 0.2 M ammonium sulfate, 100 mM Tris-HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2018 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9677 Å / Relative weight: 1 |
Reflection | Resolution: 1.43→50 Å / Num. obs: 39193 / % possible obs: 99.1 % / Redundancy: 5.3 % / CC1/2: 0.998 / Rpim(I) all: 0.043 / Rrim(I) all: 0.1 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.43→1.48 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3704 / CC1/2: 0.43 / Rpim(I) all: 0.751 / Rrim(I) all: 1.719 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ATI Resolution: 1.432→43.812 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.054 / SU ML: 0.039 / Cross valid method: FREE R-VALUE / ESU R: 0.068 / ESU R Free: 0.068 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.097 Å2
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Refinement step | Cycle: LAST / Resolution: 1.432→43.812 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: 20
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