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- PDB-1s84: PORCINE TRYPSIN COVALENT COMPLEX WITH 4-AMINO BUTANOL, BORATE AND... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1s84 | ||||||
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Title | PORCINE TRYPSIN COVALENT COMPLEX WITH 4-AMINO BUTANOL, BORATE AND ETHYLENE GLYCOL | ||||||
![]() | TRYPSIN | ||||||
![]() | HYDROLASE / SERINE PROTEASE | ||||||
Function / homology | ![]() trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Transue, T.R. / Krahn, J.M. / Gabel, S.A. / Derose, E.F. / London, R.E. | ||||||
![]() | ![]() Title: X-ray and NMR characterization of covalent complexes of trypsin, borate, and alcohols. Authors: Transue, T.R. / Krahn, J.M. / Gabel, S.A. / DeRose, E.F. / London, R.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 109.8 KB | Display | ![]() |
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PDB format | ![]() | 88.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 444.7 KB | Display | ![]() |
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Full document | ![]() | 444.7 KB | Display | |
Data in XML | ![]() | 14.2 KB | Display | |
Data in CIF | ![]() | 21.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1s5sC ![]() 1s6fC ![]() 1s6hC ![]() 1s81C ![]() 1s82C ![]() 1s83C ![]() 1s85C ![]() 1aksS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23493.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 5 types, 287 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DYB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/DYB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-DYB / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.54 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.8M MgCl2, 50mM HEPES, 5mM CaCl2, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 13, 2002 / Details: MSC/YALE DOUBLE FOCUSING MIRRORS |
Radiation | Monochromator: MSC/YALE DOUBLE FOCUSING MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→100 Å / Num. all: 17547 / Num. obs: 17547 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.649 % / Rsym value: 0.092 / Net I/σ(I): 20.6369 |
Reflection shell | Resolution: 1.85→1.92 Å / Redundancy: 6.62 % / Mean I/σ(I) obs: 4.795 / Num. unique all: 1719 / Rsym value: 0.411 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.85 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.092 |
Reflection shell | *PLUS Rmerge(I) obs: 0.411 / Mean I/σ(I) obs: 4.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1AKS Resolution: 1.85→100 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: AMBER98
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Displacement parameters | Biso mean: 17.39 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→100 Å
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Refine LS restraints |
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Refinement | *PLUS % reflection Rfree: 5 % | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |