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Yorodumi- PDB-3ail: Crystal structure of a HSL-like carboxylesterase from Sulfolobus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ail | ||||||
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Title | Crystal structure of a HSL-like carboxylesterase from Sulfolobus tokodaii complexed with paraoxon | ||||||
Components | 303aa long hypothetical esterase | ||||||
Keywords | HYDROLASE / Carboxylesterase / thermophilic / dimer / archaea | ||||||
Function / homology | Function and homology information carboxylesterase / carboxylesterase activity / identical protein binding Similarity search - Function | ||||||
Biological species | Sulfolobus tokodaii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å | ||||||
Authors | Angkawidjaja, C. / Kanaya, S. | ||||||
Citation | Journal: Febs J. / Year: 2012 Title: Structure and stability of a thermostable carboxylesterase from the thermoacidophilic archaeon Sulfolobustokodaii Authors: Angkawidjaja, C. / Koga, Y. / Takano, K. / Kanaya, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ail.cif.gz | 245.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ail.ent.gz | 196.1 KB | Display | PDB format |
PDBx/mmJSON format | 3ail.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ai/3ail ftp://data.pdbj.org/pub/pdb/validation_reports/ai/3ail | HTTPS FTP |
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-Related structure data
Related structure data | 3aikSC 3aimC 3ainC 3aioC 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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Unit cell |
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-Components
#1: Protein | Mass: 36012.949 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Strain: 7 / Gene: ST0071 / Plasmid: pET28a+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CodonPlus / References: UniProt: Q976W8, carboxylesterase #2: Chemical | ChemComp-DEP / #3: Chemical | ChemComp-MRD / ( #4: Chemical | ChemComp-PO4 / #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: 2.93 Å3/Da / Density % sol: 58 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1M Tris-HCl pH 8.5, 0.2M Ammonium phosphate monobasic, 50% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 4, 2009 |
Radiation | Monochromator: Rh-coated 1-m-long mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→50 Å / Num. all: 221504 / Num. obs: 123521 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.049 / Rsym value: 0.035 / Net I/σ(I): 23.2 |
Reflection shell | Resolution: 1.91→1.98 Å / Redundancy: 3 % / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 3.6 / Num. unique all: 21924 / Rsym value: 0.276 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3AIK Resolution: 1.91→28.07 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.378 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 25.094 Å2
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Refinement step | Cycle: LAST / Resolution: 1.91→28.07 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.91→1.959 Å / Total num. of bins used: 20
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