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- PDB-3puh: Cocaine Esterase, wild-type biologically active dimer -

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Basic information

Entry
Database: PDB / ID: 3puh
TitleCocaine Esterase, wild-type biologically active dimer
ComponentsCocaine esterase
KeywordsHYDROLASE / 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
alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily ...alpha-amino acid ester hydrolase ( Helical cap domain) / alpha-amino acid ester hydrolase ( Helical cap domain) / CocE/Serine esterase / Xaa-Pro dipeptidyl-peptidase, C-terminal / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / X-Pro dipeptidyl-peptidase C-terminal non-catalytic domain / Xaa-Pro dipeptidyl-peptidase-like domain / X-Pro dipeptidyl-peptidase (S15 family) / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Jelly Rolls / Sandwich / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsNance, M.R. / Tesmer, J.J.G.
CitationJournal: 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
DepositionDec 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cocaine esterase
B: Cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,0819
Polymers127,4202
Non-polymers6617
Water14,016778
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-42 kcal/mol
Surface area46180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.345, 105.442, 224.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 600
2114B1 - 600
DetailsThe biological assembly is a homodimer of CocE, consisting of chain A and chain B.

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Components

#1: Protein Cocaine esterase /


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 ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 778 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.41 Å3/Da / Density % sol: 63.89 %
Crystal growTemperature: 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

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.033 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.3-2.386.40.6177411.1341100
2.38-2.486.90.49277211.1381100
2.48-2.597.80.39477441.111100
2.59-2.738.30.31877901.141100
2.73-2.98.30.24477411.2291100
2.9-3.128.30.18778521.5371100
3.12-3.438.30.14178171.4991100
3.43-3.938.20.10478841.8241100
3.93-4.948.10.07579572.1881100
4.94-257.80.05882441.9691100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4 Å24.86 Å
Translation4 Å24.86 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.2492 3947 5 %RANDOM
Rwork0.2079 ---
obs0.21 78375 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 71.8 Å2 / Biso mean: 22.9962 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8741 0 38 778 9557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229076
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.95312423
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15151163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4723.728405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.318151335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5461565
X-RAY DIFFRACTIONr_chiral_restr0.0870.21391
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217071
X-RAY DIFFRACTIONr_mcbond_it0.3021.55749
X-RAY DIFFRACTIONr_mcangle_it0.56529286
X-RAY DIFFRACTIONr_scbond_it0.71533327
X-RAY DIFFRACTIONr_scangle_it1.2384.53137
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 4305 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.20.5
MEDIUM THERMAL0.242
LS refinement shellResolution: 2.3→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 320 -
Rwork0.25 5221 -
all-5541 -
obs--97.78 %

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