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Yorodumi- PDB-7bry: Bovine Pancreatic Trypsin with 6-Methoxytryptamine (Room Temperature) -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bry | ||||||
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Title | Bovine Pancreatic Trypsin with 6-Methoxytryptamine (Room Temperature) | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE / microfluidic device / crystal sorting / room temperature | ||||||
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 / molecular replacement / Resolution: 1.65 Å | ||||||
Authors | Maeki, M. / Ito, S. / Takeda, R. / Funakubo, T. / Ueno, G. / Ishida, A. / Tani, H. / Yamamoto, M. / Tokeshi, M. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Chem Sci / Year: 2020 Title: Room-temperature crystallography using a microfluidic protein crystal array device and its application to protein-ligand complex structure analysis. Authors: Maeki, M. / Ito, S. / Takeda, R. / Ueno, G. / Ishida, A. / Tani, H. / Yamamoto, M. / Tokeshi, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bry.cif.gz | 63 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bry.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 7bry.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/br/7bry ftp://data.pdbj.org/pub/pdb/validation_reports/br/7bry | HTTPS FTP |
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-Related structure data
Related structure data | 7brvC 7brwC 7brxC 7brzC 7bs0C 7bs1C 7bs2C 7bs3C 7bs4C 7bs5C 7bs6C 7bs7C 7bs8C 7bs9C 7bsaC 1s0qS 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-F5X / |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.23 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: May 9, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.5→43.62 Å / Num. obs: 33584 / % possible obs: 95.9 % / Redundancy: 6.556 % / Biso Wilson estimate: 23.431 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.182 / Rrim(I) all: 0.196 / Χ2: 0.931 / Net I/σ(I): 7.27 / Num. measured all: 220181 / Scaling rejects: 69 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1s0q Resolution: 1.65→43.62 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.61
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 66.37 Å2 / Biso mean: 19.3037 Å2 / Biso min: 7.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.65→43.62 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9
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