+Open data
-Basic information
Entry | Database: PDB / ID: 3puh | ||||||
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Title | Cocaine Esterase, wild-type biologically active dimer | ||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 | 3puh.cif.gz | 243.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3puh.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 3puh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/3puh ftp://data.pdbj.org/pub/pdb/validation_reports/pu/3puh | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Details | The biological assembly is a homodimer of CocE, consisting of chain A and chain B. |
-Components
#1: Protein | Mass: 63710.094 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | ChemComp-SO4 / #4: 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: 3.41 Å3/Da / Density % sol: 63.89 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 20% PEG 3350, 100 mM MES pH 6.0, 1 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 16, 2008 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→25 Å / Num. obs: 78491 / % possible obs: 100 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.134 / Χ2: 1.495 / Net I/σ(I): 6.7 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.908 / WRfactor Rfree: 0.2246 / WRfactor Rwork: 0.1876 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8285 / SU B: 5.957 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2518 / SU Rfree: 0.2096 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.21 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.8 Å2 / Biso mean: 22.9962 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4305 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.355 Å / Total num. of bins used: 20
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