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Yorodumi- PDB-5fxl: Structure of trypsin solved by MR from data collected by Direct D... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5fxl | ||||||
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Title | Structure of trypsin solved by MR from data collected by Direct Data Collection (DDC) using the ESRF RoboDiff goniometer | ||||||
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: 1.78 Å | ||||||
Authors | Bowler, M.W. / Nurizzo, D. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2016 Title: Robodiff: Combining a Sample Changer and Goniometer for Highly Automated Macromolecular Crystallography Experiments. Authors: Nurizzo, D. / Bowler, M.W. / Caserotto, H. / Dobias, F. / Giraud, T. / Surr, J. / Guichard, N. / Papp, G. / Guijarro, M. / Mueller-Dieckmann, C. / Flot, D. / Mcsweeney, S. / Cipriani, F. / ...Authors: Nurizzo, D. / Bowler, M.W. / Caserotto, H. / Dobias, F. / Giraud, T. / Surr, J. / Guichard, N. / Papp, G. / Guijarro, M. / Mueller-Dieckmann, C. / Flot, D. / Mcsweeney, S. / Cipriani, F. / Theveneau, P. / Leonard, G.A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fxl.cif.gz | 98.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fxl.ent.gz | 74.7 KB | Display | PDB format |
PDBx/mmJSON format | 5fxl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fx/5fxl ftp://data.pdbj.org/pub/pdb/validation_reports/fx/5fxl | HTTPS FTP |
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-Related structure data
Related structure data | 5fxmC 5fxnC 4i8gS C: citing same article (ref.) S: Starting model for refinement |
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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-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: 2.67 Å3/Da / Density % sol: 53.88 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 19, 2015 / Details: BE CRL |
Radiation | Monochromator: C110 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→47.5 Å / Num. obs: 26622 / % possible obs: 98.9 % / Observed criterion σ(I): 3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.02 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.78→1.85 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.6 / % possible all: 93.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4I8G Resolution: 1.78→47.49 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / SU B: 5.567 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.826 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→47.49 Å
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Refine LS restraints |
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