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- PDB-6svz: Reference structure of bovine trypsin (even frames of crystal x34) -
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Open data
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Basic information
Entry | Database: PDB / ID: 6svz | |||||||||
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Title | Reference structure of bovine trypsin (even frames of crystal x34) | |||||||||
![]() | Cationic trypsin | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | 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 | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 112.2 KB | Display | ![]() |
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PDB format | ![]() | 89.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6suxC ![]() 6sv0C ![]() 6sv6C ![]() 6sv8C ![]() 6sv9C ![]() 6svbC ![]() 6svdC ![]() 6svgC ![]() 6sviC ![]() 6svjC ![]() 6svnC ![]() 6svrC ![]() 6svuC ![]() 6svvC ![]() 6svwC ![]() 6svxC ![]() 6sw0C ![]() 418gS S: Starting model for refinement C: citing same article ( |
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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
#1: Protein | Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() | ||||
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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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.54 % |
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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 ...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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→42.821 Å / Num. obs: 123675 / % possible obs: 91 % / Redundancy: 4.615 % / Biso Wilson estimate: 13.614 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.108 / Rrim(I) all: 0.121 / Χ2: 1.16 / Net I/σ(I): 8.64 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 418G Resolution: 1.15→42.82 Å / Cross valid method: FREE R-VALUE
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Displacement parameters | Biso mean: 14.03 Å2 | ||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→42.82 Å
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