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- PDB-1l7r: Tyr44Phe Mutant of Bacterial Cocaine Esterase cocE -

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Basic information

Entry
Database: PDB / ID: 1l7r
TitleTyr44Phe Mutant of Bacterial Cocaine Esterase cocE
Componentscocaine esterase
KeywordsHYDROLASE / Bacterial cocaine esterase. Mutant of oxyanion hole. Hydrolase.
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. MB1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsTurner, J.M. / Larsen, N.A. / Basran, A. / Barbas III, C.F. / Bruce, N.C. / Wilson, I.A. / Lerner, R.A.
CitationJournal: Biochemistry / Year: 2002
Title: Biochemical characterization and structural analysis of a highly proficient cocaine esterase.
Authors: Turner, J.M. / Larsen, N.A. / Basran, A. / Barbas III, C.F. / Bruce, N.C. / Wilson, I.A. / Lerner, R.A.
History
DepositionMar 16, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cocaine esterase


Theoretical massNumber of molelcules
Total (without water)62,1671
Polymers62,1671
Non-polymers00
Water10,665592
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.193, 106.193, 220.872
Angle α, β, γ (deg.)90, 90, 120
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein cocaine esterase / / cocE


Mass: 62167.352 Da / Num. of mol.: 1 / Mutation: Y44F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. MB1 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L9D7, carboxylesterase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 592 / 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: 2.89 Å3/Da / Density % sol: 57.44 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10mM Tris, 25mM NaCl, 1.4-1.6M ammonium sulfate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 296K
Crystal grow
*PLUS
Method: microdialysis / Details: Larsen, N.A., (2002) Nature Struct. Biol., 9, 17.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris11pH7.5
225 mM11NaCl
310 mMdithiothreitol11
440 mg/mlprotein11
51.5-1.8 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 26, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.64→30 Å / Num. all: 91569 / Num. obs: 91569 / % possible obs: 97.1 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.8 / Rmerge(I) obs: 0.048
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.8 / % possible all: 74.4
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 6.3 %
Reflection shell
*PLUS
% possible obs: 74.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JU4

1ju4


Resolution: 1.64→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.21 4578 RANDOM
Rwork0.19 --
all0.19 91569 -
obs0.19 91569 -
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.64→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4370 0 0 592 4962
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9

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