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Yorodumi- PDB-1utm: Trypsin specificity as elucidated by LIE calculations, X-ray stru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1utm | ||||||
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Title | Trypsin specificity as elucidated by LIE calculations, X-ray structures and association constant measurements | ||||||
Components | TRYPSIN I | ||||||
Keywords | HYDROLASE / TRYPSIN / INHIBITOR SPECIFICITY / ELECTROSTATIC INTERACTIONS / COLD-ADAPTATION / MOLECULAR DYNAMICS / BINDING FREE ENERGY | ||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding Similarity search - Function | ||||||
Biological species | SALMO SALAR (Atlantic salmon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.5 Å | ||||||
Authors | Leiros, H.-K.S. / Brandsdal, B.O. / Andersen, O.A. / Os, V. / Leiros, I. / Helland, R. / Otlewski, J. / Willassen, N.P. / Smalas, A.O. | ||||||
Citation | Journal: Protein Sci. / Year: 2004 Title: Trypsin Specificity as Elucidated by Lie Calculations, X-Ray Structures, and Association Constant Measurements Authors: Leiros, H.-K.S. / Brandsdal, B.O. / Andersen, O.A. / Os, V. / Leiros, I. / Helland, R. / Otlewski, J. / Willassen, N.P. / Smalas, A.O. | ||||||
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 | 1utm.cif.gz | 54.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1utm.ent.gz | 42.2 KB | Display | PDB format |
PDBx/mmJSON format | 1utm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ut/1utm ftp://data.pdbj.org/pub/pdb/validation_reports/ut/1utm | HTTPS FTP |
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-Related structure data
Related structure data | 1utjC 1utkC 1utlC 1utnC 1utoC 1utpC 1utqC 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: 25998.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SALMO SALAR (Atlantic salmon) / Organ: PYLORIC CAECA / References: UniProt: P35031, trypsin |
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#2: Chemical | ChemComp-PEA / |
#3: Chemical | ChemComp-CA / |
#4: 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: 1.97 Å3/Da / Density % sol: 37.67 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6 / Details: pH 6.00 | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 37 ℃ / pH: 6 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.07 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→8 Å / Num. obs: 32883 / % possible obs: 97.9 % / Redundancy: 3.39 % / Biso Wilson estimate: 14.25 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.1 |
Reflection shell | Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 / % possible all: 93.4 |
Reflection | *PLUS Highest resolution: 1.5 Å / Num. measured all: 111508 / Rmerge(I) obs: 0.048 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.8 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 15.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.17 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→8 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 8 Å / % reflection Rfree: 7 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |