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Yorodumi- PDB-3ida: Thermostable Cocaine Esterase with mutations L169K and G173Q, bou... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ida | ||||||
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Title | Thermostable Cocaine Esterase with mutations L169K and G173Q, bound to DTT adduct | ||||||
Components | Cocaine esterase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / esterase | ||||||
Function / homology | Function and homology information cocaine esterase / cocaine catabolic process / carboxylic ester hydrolase activity / dipeptidyl-peptidase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Rhodococcus sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Difference fourier / Resolution: 1.6 Å | ||||||
Authors | Tesmer, J.J.G. / Nance, M.R. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2010 Title: A thermally stable form of bacterial cocaine esterase: a potential therapeutic agent for treatment of cocaine abuse. Authors: Brim, R.L. / Nance, M.R. / Youngstrom, D.W. / Narasimhan, D. / Zhan, C.G. / Tesmer, J.J. / Sunahara, R.K. / Woods, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ida.cif.gz | 150.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ida.ent.gz | 116.8 KB | Display | PDB format |
PDBx/mmJSON format | 3ida.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/id/3ida ftp://data.pdbj.org/pub/pdb/validation_reports/id/3ida | HTTPS FTP |
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-Related structure data
Related structure data | 1ju3S 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: 63797.195 Da / Num. of mol.: 1 / Mutation: L169K, T172R Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: MB1 / Gene: cocE / Plasmid: pET-22 (b) + / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Gold References: UniProt: Q9L9D7, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||||||
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#2: Chemical | #3: Chemical | ChemComp-DBC / ( | #4: Chemical | ChemComp-GOL / #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: 3.01 Å3/Da / Density % sol: 59.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 1.7 M ammonium sulfate, 25 mM NaCl, 10 mM Tris pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.02 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.02 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. all: 104076 / Num. obs: 103956 / % possible obs: 99.1 % / Redundancy: 5 % / Rsym value: 0.094 / Net I/σ(I): 22.4 |
-Processing
Software |
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Refinement | Method to determine structure: Difference fourier Starting model: 1ju3 Resolution: 1.6→24.59 Å / Cor.coef. Fo:Fc: 0.964 / SU B: 1.149 / SU ML: 0.041 / ESU R: 0.074 / 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: 18.658 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→24.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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