+Open data
-Basic information
Entry | Database: PDB / ID: 1tio | |||||||||
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Title | HIGH PACKING DENSITY FORM OF BOVINE BETA-TRYPSIN IN CYCLOHEXANE | |||||||||
Components | PROTEIN (BETA-TRYPSIN) | |||||||||
Keywords | HYDROLASE / SERINE PROTEASE / BENZAMIDINE INHIBITED | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.93 Å | |||||||||
Authors | Huang, Q. / Zhu, G. / Wang, Z. / Tang, Q. | |||||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 1998 Title: X-ray studies on two forms of bovine beta-trypsin crystals in neat cyclohexane. Authors: Zhu, G. / Huang, Q. / Wang, Z. / Qian, M. / Jia, Y. / Tang, Y. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tio.cif.gz | 60.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tio.ent.gz | 42 KB | Display | PDB format |
PDBx/mmJSON format | 1tio.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ti/1tio ftp://data.pdbj.org/pub/pdb/validation_reports/ti/1tio | HTTPS FTP |
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-Related structure data
Related structure data | 2tioC 1btyS 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23324.287 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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-Non-polymers , 5 types, 184 molecules
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-CHX / | #6: 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: 2.3 Å3/Da / Density % sol: 46 % Description: TRYPSIN CRYSTAL WAS SOAKED IN CYCLOHEXANE 12 HOURS BEFORE DATA COLLECTION | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.2 Details: HANGING DROP METHOD: THE PROTEIN WAS DISSOLVED IN 10 MM HAC-NAAC BUFFER (PH 4.1) PRECIPITANT AND RESERVOIR SOLUTION WERE 0.5 M NA2SO4 AND 0.1 M SODIUM CACODYLATE-HCL BUFFER CONTAINING 15% ...Details: HANGING DROP METHOD: THE PROTEIN WAS DISSOLVED IN 10 MM HAC-NAAC BUFFER (PH 4.1) PRECIPITANT AND RESERVOIR SOLUTION WERE 0.5 M NA2SO4 AND 0.1 M SODIUM CACODYLATE-HCL BUFFER CONTAINING 15% (W/V) MGSO4 AND 1.5% (V/V) MPD AT PH 6.2., vapor diffusion - hanging drop PH range: 4.1-6.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 4.1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Date: Apr 15, 1996 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→64 Å / Num. obs: 14880 / % possible obs: 88 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 12 |
Reflection | *PLUS % possible obs: 88 % / Num. measured all: 34500 |
-Processing
Software | Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BTY Resolution: 1.93→8 Å / Rfactor Rfree error: 0.006 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.93→2.02 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.224 / Rfactor Rwork: 0.225 |