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- PDB-3i2i: Cocaine Esterase with mutation T172R, bound to DTT adduct -

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Basic information

Entry
Database: PDB / ID: 3i2i
TitleCocaine Esterase with mutation T172R, bound to DTT adduct
ComponentsCocaine esterase
KeywordsHYDROLASE / alpha/beta 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 ...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
(4S,5S)-4,5-BIS(MERCAPTOMETHYL)-1,3-DIOXOLAN-2-OL / Cocaine esterase
Similarity search - Component
Biological speciesRhodococcus sp. MB1 'Bresler 1999' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Difference fourier / Resolution: 2.14 Å
AuthorsTesmer, J.J.G. / Nance, M.R.
CitationJournal: Protein Eng.Des.Sel. / Year: 2010
Title: Structural analysis of thermostabilizing mutations of cocaine esterase.
Authors: Narasimhan, D. / Nance, M.R. / Gao, D. / Ko, M.C. / Macdonald, J. / Tamburi, P. / Yoon, D. / Landry, D.M. / Woods, J.H. / Zhan, C.G. / Tesmer, J.J. / Sunahara, R.K.
History
DepositionJun 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)64,56913
Polymers63,7661
Non-polymers80312
Water9,080504
1
A: Cocaine esterase
hetero molecules

A: Cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,13826
Polymers127,5322
Non-polymers1,60624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area6890 Å2
ΔGint-132 kcal/mol
Surface area38500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.282, 106.282, 219.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Cocaine esterase


Mass: 63766.188 Da / Num. of mol.: 1 / Mutation: T172R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. MB1 'Bresler 1999' (bacteria)
Strain: MB1 / Gene: Cocaine Esterase, cocE / Plasmid: pET-22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Gold (DE3)
References: UniProt: Q9L9D7, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

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Non-polymers , 5 types, 516 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DBC / (4S,5S)-4,5-BIS(MERCAPTOMETHYL)-1,3-DIOXOLAN-2-OL


Mass: 182.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O3S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.82 Å3/Da / Density % sol: 56.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mM Tris pH 7.5, 25 mM NaCl, 1.6 M Ammonium Sulfate, 10mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9792 Å
DetectorDate: Apr 5, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 38215 / % possible obs: 87.5 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.1-2.1860.504135.3
2.18-2.267.50.462191.8
2.26-2.378.50.436194
2.37-2.499.50.375195
2.49-2.6510.40.305195
2.65-2.8510.60.219194.6
2.85-3.1410.70.158194
3.14-3.5910.90.108193.1
3.59-4.52110.096192
4.52-5011.10.072189.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: Difference fourier
Starting model: PDB: 1JU3

1ju3


Resolution: 2.14→19.94 Å / Cor.coef. Fo:Fc: 0.968 / SU B: 2.947 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18 1927 5.1 %RANDOM
Rwork0.15899 ---
obs0.15899 38098 92.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.598 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.14→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 40 504 4922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224867
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.9596687
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3545640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11223.744219
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02615726
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.281537
X-RAY DIFFRACTIONr_chiral_restr0.0880.2743
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023854
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.22323
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.23301
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2547
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.267
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1460.231
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6341.53151
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0825006
X-RAY DIFFRACTIONr_scbond_it1.64831949
X-RAY DIFFRACTIONr_scangle_it2.6874.51681
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.195 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.194 2529 -
Rfree-0 -
obs--85.93 %
Refinement TLS params.Method: refined / Origin x: 15.808 Å / Origin y: 64.846 Å / Origin z: -0.254 Å
111213212223313233
T-0.0448 Å20.0128 Å20.0066 Å2--0.0729 Å20.0043 Å2---0.0608 Å2
L0.7115 °20.1102 °20.0375 °2-0.4923 °20.0985 °2--0.6736 °2
S0.0204 Å °-0.0986 Å °0.0314 Å °0.0314 Å °0.0001 Å °0.0259 Å °0.0075 Å °0.009 Å °-0.0206 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 574
2X-RAY DIFFRACTION1A588 - 596
3X-RAY DIFFRACTION1A597 - 599

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