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Yorodumi- PDB-3t52: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Le... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t52 | ||||||
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Title | L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity | ||||||
Components | Arylesterase | ||||||
Keywords | OXIDOREDUCTASE / HYDRLOASE / peptide flip | ||||||
Function / homology | Function and homology information arylesterase / Oxidoreductases / peroxidase activity / arylesterase activity Similarity search - Function | ||||||
Biological species | Pseudomonas fluorescens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | ||||||
Authors | Kazlauskas, R.J. / Yin, T. / Purpero, V.M. | ||||||
Citation | Journal: To be Published Title: L29I Mutation in an Aryl Esterase from Pseudomonas fluorescens Leads to Unique Peptide Flip and Increased Activity Authors: Yin, T. / Kazlauskas, R.J. / Purpero, V.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t52.cif.gz | 365.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t52.ent.gz | 297.9 KB | Display | PDB format |
PDBx/mmJSON format | 3t52.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/3t52 ftp://data.pdbj.org/pub/pdb/validation_reports/t5/3t52 | HTTPS FTP |
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-Related 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
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 29993.955 Da / Num. of mol.: 6 / Mutation: L29I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: SIK WI / Plasmid: pL29I / Production host: Escherichia coli (E. coli) / Strain (production host): Dh5 alpha / References: UniProt: P22862, arylesterase, Oxidoreductases |
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-Non-polymers , 6 types, 1264 molecules
#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-PEO / #6: Chemical | ChemComp-ACT / #7: 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: 4.41 Å3/Da / Density % sol: 72.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1% PEG 400, 1.65M (NH4)2SO4, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.98 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: NOIR-1 / Detector: CCD / Date: May 10, 2008 / Details: mirrors | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→48.33 Å / Num. obs: 207756 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 5.46 % / Biso Wilson estimate: 22.1 Å2 / Rmerge(I) obs: 0.111 / Χ2: 0.97 / Net I/σ(I): 6.6 / Scaling rejects: 11454 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: PDB entry IVA4 Resolution: 2→47.8 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.1936 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8321 / SU B: 2.781 / SU ML: 0.077 / SU R Cruickshank DPI: 0.1218 / SU Rfree: 0.1171 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 3 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 76.66 Å2 / Biso mean: 25.825 Å2 / Biso min: 12.68 Å2
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Refinement step | Cycle: LAST / Resolution: 2→47.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Rfactor Rfree error: 0.117 / Total num. of bins used: 20
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