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Yorodumi- PDB-5xwj: Crystal Structure of Porcine pancreatic trypsin with tripeptide i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5xwj | ||||||
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Title | Crystal Structure of Porcine pancreatic trypsin with tripeptide inhibitor, TRE, at pH 7 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / protease / inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information trypsin / digestion / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding Similarity search - Function | ||||||
Biological species | Sus scrofa (pig) Capsicum annuum (plant) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Saikhedkar, N.S. / Bhoite, A.S. / Giri, A.P. / Kulkarni, K.A. | ||||||
Funding support | India, 1items
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Citation | Journal: Insect Biochem. Mol. Biol. / Year: 2018 Title: Tripeptides derived from reactive centre loop of potato type II protease inhibitors preferentially inhibit midgut proteases of Helicoverpa armigera. Authors: Saikhedkar, N.S. / Joshi, R.S. / Bhoite, A.S. / Mohandasan, R. / Yadav, A.K. / Fernandes, M. / Kulkarni, K.A. / Giri, A.P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5xwj.cif.gz | 190.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5xwj.ent.gz | 149.8 KB | Display | PDB format |
PDBx/mmJSON format | 5xwj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xw/5xwj ftp://data.pdbj.org/pub/pdb/validation_reports/xw/5xwj | HTTPS FTP |
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-Related structure data
Related structure data | 5xw8C 5xw9C 5xwaC 5xwlC 4doqS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24428.424 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: Commercially available trypsin from Sigma (Cat. no. T4799) Source: (natural) Sus scrofa (pig) / References: UniProt: P00761, trypsin #2: Protein/peptide | Mass: 431.464 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Capsicum annuum (plant) #3: Chemical | #4: Chemical | ChemComp-MPD / ( | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.84 Å3/Da / Density % sol: 67.96 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES pH7.5, 70% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 9, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→47.89 Å / Num. obs: 67984 / % possible obs: 99.8 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.11 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6707 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DOQ Resolution: 1.8→42.286 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.286 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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