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Yorodumi- PDB-6sv8: Terahertz irradiated structure of bovine trypsin (odd frames of c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6sv8 | |||||||||
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Title | Terahertz irradiated structure of bovine trypsin (odd frames of crystal x38) | |||||||||
Components | Cationic trypsin | |||||||||
Keywords | HYDROLASE / bovine trypsin / Terahertz irradiation / odd frames / x38 | |||||||||
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: 1.15 Å | |||||||||
Authors | Ahlberg Gagner, V. / Lundholm, I. / Garcia-Bonete, M.J. / Rodilla, H. / Friedman, R. / Zhaunerchyk, V. / Bourenkov, G. / Schneider, T. / Stake, J. / Katona, G. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: Sci Rep / Year: 2019 Title: Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties. Authors: Gagner, V.A. / Lundholm, I. / Garcia-Bonete, M.J. / Rodilla, H. / Friedman, R. / Zhaunerchyk, V. / Bourenkov, G. / Schneider, T. / Stake, J. / Katona, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6sv8.cif.gz | 112.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6sv8.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 6sv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sv/6sv8 ftp://data.pdbj.org/pub/pdb/validation_reports/sv/6sv8 | HTTPS FTP |
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-Related structure data
Related structure data | 6suxC 6sv0C 6sv6C 6sv9C 6svbC 6svdC 6svgC 6sviC 6svjC 6svnC 6svrC 6svuC 6svvC 6svwC 6svxC 6svzC 6sw0C 418gS 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
#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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#2: Chemical | ChemComp-CA / | ||||
#3: Chemical | ChemComp-BEN / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.09 Å3/Da / Density % sol: 41.01 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: protein solution- 60 mg/ml trypsin, 6 mg/ml benzamidine and 3 mM CaCl2 in a 30 mM HEPES buffer pH 7.0. Well solution- 18% PEG 8000, 200 mM (NH4)2SO4, 50 mM HEPES pH 7, 3 mM CaCl2 and 6 mg/ml ...Details: protein solution- 60 mg/ml trypsin, 6 mg/ml benzamidine and 3 mM CaCl2 in a 30 mM HEPES buffer pH 7.0. Well solution- 18% PEG 8000, 200 mM (NH4)2SO4, 50 mM HEPES pH 7, 3 mM CaCl2 and 6 mg/ml benzamidine. 1:1 ratio drops |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.8856 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 23, 2015 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.8856 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→42.92 Å / Num. obs: 129886 / % possible obs: 96.1 % / Redundancy: 4.902 % / Biso Wilson estimate: 13.617 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.083 / Χ2: 1.15 / Net I/σ(I): 10.94 / Num. measured all: 636710 / Scaling rejects: 533 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 418G Resolution: 1.15→42.92 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 13.285 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→42.92 Å
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