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Yorodumi- PDB-6dwr: Trypsin serine protease modified with the protease inhibitor cyan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6dwr | ||||||
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Title | Trypsin serine protease modified with the protease inhibitor cyanobenzylsulfonylfluoride | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / serine protease | ||||||
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: 1.319 Å | ||||||
Authors | Luo, M. / Eaton, C.N. / Phillips-Piro, C.M. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chemistryselect / Year: 2019 Title: Paired Spectroscopic and Crystallographic Studies of Protease Active Sites Authors: Luo, M. / Eaton, C.N. / Hess, K.R. / Phillips-Piro, C.M. / Brewer, S.H. / Fenlon, E.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6dwr.cif.gz | 150.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6dwr.ent.gz | 119.1 KB | Display | PDB format |
PDBx/mmJSON format | 6dwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/6dwr ftp://data.pdbj.org/pub/pdb/validation_reports/dw/6dwr | HTTPS FTP |
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-Related structure data
Related structure data | 6dwqC 4i8gS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23809.711 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-EDO / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SO4 / | #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: 1.95 Å3/Da / Density % sol: 36.85 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 22% PEG8000, 0.225 M ammonium sulfate, 0.1 M Hepes (pH 7.5), 10% isopropanol Temp details: Room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.319→43.21 Å / Num. obs: 44011 / % possible obs: 99.8 % / Redundancy: 9.2 % / CC1/2: 0.999 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 1.319→1.34 Å / Redundancy: 6.1 % / Num. unique obs: 2070 / CC1/2: 0.441 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4I8G Resolution: 1.319→43.21 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.08
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.319→43.21 Å
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Refine LS restraints |
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LS refinement shell |
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