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- PDB-7wb7: Crystal structure of Bovine Pancreatic Trypsin in complex with Se... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7wb7 | ||||||
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Title | Crystal structure of Bovine Pancreatic Trypsin in complex with Serotonin at Room Temperature | ||||||
![]() | Cationic trypsin | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sakai, N. / Okumura, H. / Yamamoto, M. / Kumasaka, T. | ||||||
Funding support | 1items
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![]() | ![]() Title: In situ crystal data-collection and ligand-screening system at SPring-8. Authors: Okumura, H. / Sakai, N. / Murakami, H. / Mizuno, N. / Nakamura, Y. / Ueno, G. / Masunaga, T. / Kawamura, T. / Baba, S. / Hasegawa, K. / Yamamoto, M. / Kumasaka, T. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 102.9 KB | Display | ![]() |
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PDB format | ![]() | 76.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 696.6 KB | Display | ![]() |
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Full document | ![]() | 697 KB | Display | |
Data in XML | ![]() | 11.2 KB | Display | |
Data in CIF | ![]() | 15.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7wa0C ![]() 7wa2C ![]() 7wb6C ![]() 7wb8C ![]() 7wb9C ![]() 7wbaC ![]() 1s0rS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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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-SRO / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris-HCl, 30% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 29, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→50 Å / Num. obs: 38213 / % possible obs: 98.5 % / Redundancy: 4.75 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.155 / Net I/σ(I): 7.84 |
Reflection shell | Resolution: 1.45→1.54 Å / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6221 / CC1/2: 0.535 / Rrim(I) all: 1.207 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1S0R Resolution: 1.45→44.02 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.565 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.057 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.922 Å2
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Refinement step | Cycle: 1 / Resolution: 1.45→44.02 Å
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Refine LS restraints |
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