+Open data
-Basic information
Entry | Database: PDB / ID: 3pui | ||||||
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Title | Cocaine Esterase with mutations G4C, S10C | ||||||
Components | Cocaine esterase | ||||||
Keywords | HYDROLASE / alpha/beta hydrolase / jelly-roll beta-barrel / Cleavage of cocaine | ||||||
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 / PDB ENTRY 1JU3 / Resolution: 1.53 Å | ||||||
Authors | Nance, M.R. / Tesmer, J.J.G. | ||||||
Citation | Journal: Mol.Pharmacol. / Year: 2011 Title: Subunit stabilization and polyethylene glycolation of cocaine esterase improves in vivo residence time. Authors: Narasimhan, D. / Collins, G.T. / Nance, M.R. / Nichols, J. / Edwald, E. / Chan, J. / Ko, M.C. / Woods, J.H. / Tesmer, J.J. / Sunahara, R.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pui.cif.gz | 268.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pui.ent.gz | 217.4 KB | Display | PDB format |
PDBx/mmJSON format | 3pui.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/3pui ftp://data.pdbj.org/pub/pdb/validation_reports/pu/3pui | HTTPS FTP |
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-Related structure data
Related structure data | 3puhC 1ju3S 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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Unit cell |
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-Components
#1: Protein | Mass: 63772.250 Da / Num. of mol.: 1 / Mutation: G4C, S10C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: MB1 Bresler / Gene: cocE / Plasmid: pET-22b (+) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 Gold DE3 References: UniProt: Q9L9D7, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases | ||||
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#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: 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: 2.81 Å3/Da / Density % sol: 56.23 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 10mM Tris pH 7.5, 25 mM NaCl, 1.6 M Ammonium Sulfate, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
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Detector | Date: Mar 4, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 1.53→25 Å / Num. obs: 110836 / % possible obs: 94.6 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.53→1.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.4 / Rsym value: 0.634 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: PDB ENTRY 1JU3 Starting model: 1ju3 Resolution: 1.53→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.467 / SU ML: 0.04 / SU R Cruickshank DPI: 0.0802 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.065 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.276 Å2
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Refinement step | Cycle: LAST / Resolution: 1.53→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.53→1.57 Å / Total num. of bins used: 20
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