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- PDB-7f65: Bacetrial Cocaine Esterase with mutations T172R/G173Q/V116K/S117A... -

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Basic information

Entry
Database: PDB / ID: 7f65
TitleBacetrial Cocaine Esterase with mutations T172R/G173Q/V116K/S117A/A51L, bound to benzoic acid
ComponentsCocaine esterase
KeywordsHYDROLASE / Cocaine esterase / mutantions / benzoylecgonine metabolism
Function / homology
Function and homology information


cocaine esterase / cocaine catabolic process / carboxylic ester hydrolase activity / dipeptidyl-peptidase 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. MB1 'Bresler 1999' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.202 Å
AuthorsOuyang, P.F. / Zhang, Y. / Tong, J.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Computational Design and Crystal Structure of a Highly Efficient Benzoylecgonine Hydrolase.
Authors: Chen, X. / Deng, X. / Zhang, Y. / Wu, Y. / Yang, K. / Li, Q. / Wang, J. / Yao, W. / Tong, J. / Xie, T. / Hou, S. / Yao, J.
History
DepositionJun 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: Cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5853
Polymers62,3671
Non-polymers2182
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-15 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.022, 106.022, 222.284
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Cocaine esterase


Mass: 62366.648 Da / Num. of mol.: 1 / Fragment: Cocaine esterase / Mutation: T172R/G173Q/V116K/S117A/A51L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. MB1 'Bresler 1999' (bacteria)
Strain: MB1 Bresler / Gene: cocE / Production host: Rhodococcus sp. MB1 (bacteria) / References: UniProt: Q9L9D7, cocaine esterase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.88 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 292 K / Method: evaporation / pH: 6.5 / Details: 0.1 M MES pH 6.5, 1.75 M AMS, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 0.987 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 38298 / % possible obs: 100 % / Redundancy: 33.7 % / Biso Wilson estimate: 24.72 Å2 / Rmerge(I) obs: 0.316 / Rpim(I) all: 0.054 / Rrim(I) all: 0.321 / Χ2: 0.493 / Net I/σ(I): 1.9 / Num. measured all: 1290075
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.2421.21.10418640.870.2431.1310.445100
2.24-2.28231.0818650.9060.2281.1040.456100
2.28-2.3224.31.0618780.9050.2171.0830.447100
2.32-2.3724.41.02718540.9210.211.0490.45199.9
2.37-2.4224.20.87618870.9420.1790.8940.455100
2.42-2.4829.50.97518840.9470.1810.9920.464100
2.48-2.5433.40.88818750.960.1550.9020.458100
2.54-2.6135.70.90518640.9660.1530.9180.459100
2.61-2.6937.60.85918910.9720.1410.8710.463100
2.69-2.7739.20.79118970.9790.1270.8020.462100
2.77-2.8739.90.67619130.9860.1070.6850.471100
2.87-2.9939.80.58818750.9880.0930.5950.471100
2.99-3.1239.50.46619200.9910.0750.4720.477100
3.12-3.2937.80.35318990.9950.0580.3570.493100
3.29-3.4933.30.2519090.9960.0440.2540.513100
3.49-3.7638.40.20319380.9960.0330.2060.538100
3.76-4.1440.40.16519400.9960.0260.1670.564100
4.14-4.7439.70.12919640.9980.020.1310.56799.9
4.74-5.9736.80.1420130.9950.0230.1420.538100
5.97-5034.10.121680.9990.0170.1010.558100

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å24.08 Å
Translation2.5 Å24.08 Å

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHASER2.6.0phasing
PHENIX1.10.1-2155refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JU4

1ju4


Resolution: 2.202→24.083 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.208 2000 5.25 %
Rwork0.172 36084 -
obs0.1739 38084 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 72.24 Å2 / Biso mean: 14.6818 Å2 / Biso min: 9.23 Å2
Refinement stepCycle: final / Resolution: 2.202→24.083 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4387 0 14 342 4743
Biso mean--19.08 15.84 -
Num. residues----573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064508
X-RAY DIFFRACTIONf_angle_d0.8536162
X-RAY DIFFRACTIONf_chiral_restr0.053689
X-RAY DIFFRACTIONf_plane_restr0.005812
X-RAY DIFFRACTIONf_dihedral_angle_d13.7662642
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.202-2.25680.26741400.20312526100
2.2568-2.31780.20831400.18942514100
2.3178-2.38590.22271400.19792541100
2.3859-2.46280.24841400.19132536100
2.4628-2.55080.24411420.19222542100
2.5508-2.65280.26341410.1932550100
2.6528-2.77330.2271410.18892541100
2.7733-2.91930.19671410.18492557100
2.9193-3.10190.24271430.19032568100
3.1019-3.34080.23811430.17962585100
3.3408-3.67590.1881440.1652590100
3.6759-4.20540.16871440.1482609100
4.2054-5.28910.16021470.14022654100
5.2891-24.0830.20761540.1624277198
Refinement TLS params.Method: refined / Origin x: 37.0389 Å / Origin y: 26.789 Å / Origin z: -0.2906 Å
111213212223313233
T0.1335 Å20.0059 Å2-0.0152 Å2-0.1072 Å2-0.0007 Å2--0.1223 Å2
L0.2703 °20.1208 °2-0.078 °2-0.2493 °2-0.0151 °2--0.3337 °2
S0.02 Å °-0.0456 Å °-0.0064 Å °0.0301 Å °-0.0016 Å °-0.0357 Å °-0.0121 Å °0.0051 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 1002
2X-RAY DIFFRACTION1allA1001
3X-RAY DIFFRACTION1allS1 - 824

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