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- PDB-9k48: Bacetrial Cocaine Esterase with mutations T172R/G173Q/V116K/S117A/A51K -

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Basic information

Entry
Database: PDB / ID: 9k48
TitleBacetrial Cocaine Esterase with mutations T172R/G173Q/V116K/S117A/A51K
ComponentsCocaine esterase
KeywordsHYDROLASE / Cocaine esterase / BE specificity
Function / homology
Function and homology information


cocaine esterase / cocaine catabolic process / dipeptidyl-peptidase activity / carboxylic ester hydrolase activity / cytoplasm
Similarity search - Function
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-like domain superfamily / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
BENZOIC ACID / Cocaine esterase
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.249 Å
AuthorsZhang, Y. / Tong, J.S.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32101010 China
Ministry of Science and Technology (MoST, China)2022ZD0214600 China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Catalytic mechanism, computational design, and crystal structure of a highly specific and efficient benzoylecgonine hydrolase.
Authors: Chen, X. / Zhang, Y. / Tong, J. / Ouyang, P. / Deng, X. / Zhang, J. / Liu, H. / Hu, Y. / Yao, W. / Wang, J. / Wang, X. / Hou, S. / Yao, J.
History
DepositionOct 21, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5052
Polymers62,3831
Non-polymers1221
Water8,107450
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cocaine esterase
hetero molecules

A: Cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,0104
Polymers124,7652
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area3390 Å2
ΔGint3 kcal/mol
Surface area38360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.959, 105.959, 221.997
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cocaine esterase


Mass: 62382.672 Da / Num. of mol.: 1 / Mutation: T172R/G173Q/V116K/S117A/A51K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (strain MB1 Bresler) (bacteria)
Gene: cocE / Plasmid: plasmid / Details (production host): pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9L9D7, cocaine esterase
#2: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 57.38 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.5 / Details: 0.1 M MES, pH 6.5, 1.8 M AMS, 10% glycerol / Temp details: 19 degree

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.249→50 Å / Num. obs: 35828 / % possible obs: 99.6 % / Redundancy: 14.1 % / CC1/2: 0.987 / CC star: 0.997 / Rmerge(I) obs: 0.261 / Rpim(I) all: 0.067 / Rrim(I) all: 0.27 / Χ2: 0.493 / Net I/σ(I): 10
Reflection shellResolution: 2.25→2.29 Å / Rmerge(I) obs: 0.999 / Mean I/σ(I) obs: 2 / Num. unique obs: 1735 / CC1/2: 0.817 / CC star: 0.948 / Rpim(I) all: 0.344 / Rrim(I) all: 1.061 / Χ2: 0.448

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.249→25.189 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2035 2000 5.64 %
Rwork0.1602 --
obs0.1626 35453 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.249→25.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4388 0 9 450 4847
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074505
X-RAY DIFFRACTIONf_angle_d0.8846156
X-RAY DIFFRACTIONf_dihedral_angle_d14.2732644
X-RAY DIFFRACTIONf_chiral_restr0.053688
X-RAY DIFFRACTIONf_plane_restr0.005812
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2495-2.30570.23461400.18372343X-RAY DIFFRACTION99
2.3057-2.3680.2551400.19112331X-RAY DIFFRACTION99
2.368-2.43760.19761400.17622359X-RAY DIFFRACTION99
2.4376-2.51620.24971410.17182354X-RAY DIFFRACTION100
2.5162-2.60610.2451400.17522345X-RAY DIFFRACTION100
2.6061-2.71030.2241440.17692390X-RAY DIFFRACTION100
2.7103-2.83350.2381410.17672366X-RAY DIFFRACTION100
2.8335-2.98260.22051420.17082385X-RAY DIFFRACTION100
2.9826-3.16920.2171430.17252388X-RAY DIFFRACTION100
3.1692-3.41330.20741450.1652412X-RAY DIFFRACTION100
3.4133-3.75580.18881430.14672408X-RAY DIFFRACTION100
3.7558-4.2970.1671460.13282442X-RAY DIFFRACTION100
4.297-5.40490.16891480.13652473X-RAY DIFFRACTION99
5.4049-25.1890.19571470.16732457X-RAY DIFFRACTION93

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