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Yorodumi- PDB-3qt4: Structure of digestive procathepsin L 3 of Tenebrio molitor larva... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qt4 | ||||||
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Title | Structure of digestive procathepsin L 3 of Tenebrio molitor larval midgut | ||||||
Components | Cathepsin-L-like midgut cysteine proteinase | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEINASE / ZYMOGEN / INTRAMOLECULAR DISSULPHIDE BONDS / INSECT LARVAL MIDGUT | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Tenebrio molitor (yellow mealworm) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å | ||||||
Authors | Beton, D. / Guzzo, C.R. / Terra, W.R. / Farah, C.S. | ||||||
Citation | Journal: Insect Biochem.Mol.Biol. / Year: 2012 Title: The 3D structure and function of digestive cathepsin L-like proteinases of Tenebrio molitor larval midgut. Authors: Beton, D. / Guzzo, C.R. / Ribeiro, A.F. / Farah, C.S. / Terra, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qt4.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qt4.ent.gz | 63.4 KB | Display | PDB format |
PDBx/mmJSON format | 3qt4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/3qt4 ftp://data.pdbj.org/pub/pdb/validation_reports/qt/3qt4 | HTTPS FTP |
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-Related structure data
Related structure data | 3qj3C 2o6xS C: citing same article (ref.) S: Starting model for refinement |
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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: 36483.023 Da / Num. of mol.: 1 / Mutation: C122S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tenebrio molitor (yellow mealworm) / Gene: pCAL3 / Plasmid: pAE / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B (D3) / References: UniProt: Q7YXL2, cathepsin L | ||||||
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#2: Chemical | ChemComp-PO4 / #3: Chemical | ChemComp-PG4 / #4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.1 M sodium citrate, 0.2 M ammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.42 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Apr 24, 2008 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.42 Å / Relative weight: 1 |
Reflection | Resolution: 2.11→35 Å / Num. obs: 20295 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 25.22 |
Reflection shell | Resolution: 2.11→2.19 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 6.94 / % possible all: 94.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2O6X Resolution: 2.11→26.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.697 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R Free: 0.167 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.274 Å2
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Refinement step | Cycle: LAST / Resolution: 2.11→26.23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.11→2.165 Å / Total num. of bins used: 20
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