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Yorodumi- PDB-7wb8: Crystal structure of Bovine Pancreatic Trypsin in complex with 5-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wb8 | ||||||
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Title | Crystal structure of Bovine Pancreatic Trypsin in complex with 5-Methoxytryptamine at Room Temperature | ||||||
Components | Cationic trypsin | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information cap snatching / virion component / hydrolase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / nucleotide binding / metal ion binding Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å | ||||||
Authors | Sakai, N. / Okumura, H. / Yamamoto, M. / Kumasaka, T. | ||||||
Funding support | 1items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wb8.cif.gz | 102.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wb8.ent.gz | 76 KB | Display | PDB format |
PDBx/mmJSON format | 7wb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7wb8_validation.pdf.gz | 701.4 KB | Display | wwPDB validaton report |
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Full document | 7wb8_full_validation.pdf.gz | 701.9 KB | Display | |
Data in XML | 7wb8_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 7wb8_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wb8 ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wb8 | HTTPS FTP |
-Related structure data
Related structure data | 7wa0C 7wa2C 7wb6C 7wb7C 7wb9C 7wbaC 1s0rS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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-F5U / |
#3: Chemical | ChemComp-DMS / |
#4: Chemical | ChemComp-CA / |
#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: 2.3 Å3/Da / Density % sol: 46.43 % |
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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: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 22, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.38→50 Å / Num. obs: 44589 / % possible obs: 99.3 % / Redundancy: 4.97 % / Biso Wilson estimate: 15.4 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.09 / Net I/σ(I): 11.12 |
Reflection shell | Resolution: 1.38→1.46 Å / Redundancy: 4.98 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6834 / CC1/2: 0.528 / Rrim(I) all: 1.294 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1S0R Resolution: 1.38→44.07 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.975 / SU B: 2.119 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.047 / 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: 17.151 Å2
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Refinement step | Cycle: 1 / Resolution: 1.38→44.07 Å
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