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- PDB-3i2k: Cocaine Esterase, wild type, bound to a DTT adduct -

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Basic information

Entry
Database: PDB / ID: 3i2k
TitleCocaine Esterase, wild type, bound to a 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 / 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
(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: 1.51 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 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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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)64,47712
Polymers63,7101
Non-polymers76711
Water15,529862
1
A: Cocaine esterase
hetero molecules

A: Cocaine esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,95524
Polymers127,4202
Non-polymers1,53522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Buried area6660 Å2
ΔGint-128 kcal/mol
Surface area38380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.513, 105.513, 222.377
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: 63710.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. MB1 'Bresler 1999' (bacteria)
Strain: MB1 / Gene: 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, 873 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / 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.: 862 / 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: 2.82 Å3/Da / Density % sol: 56.36 %
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: 21-ID-D / Wavelength: 1 Å
DetectorDate: Apr 14, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.51→40 Å / Num. obs: 114633 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.51-1.565.90.5441100
1.56-1.638.20.4331100
1.63-1.78.50.3221100
1.7-1.798.50.2321100
1.79-1.98.50.1531100
1.9-2.058.50.1021100
2.05-2.268.50.0761100
2.26-2.588.50.0721100
2.58-3.258.10.0721100
3.25-4080.044199.6

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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: 1.51→20 Å / Cor.coef. Fo:Fc: 0.975 / SU B: 0.842 / SU ML: 0.031 / Cross valid method: THROUGHOUT / ESU R: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.152 5722 5 %RANDOM
Rwork0.14568 ---
obs0.14568 114339 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.917 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.51→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4383 0 39 862 5284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0225068
X-RAY DIFFRACTIONr_bond_other_d0.0010.023334
X-RAY DIFFRACTIONr_angle_refined_deg1.211.9616974
X-RAY DIFFRACTIONr_angle_other_deg0.83438130
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3575675
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66123.684228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20615765
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9831540
X-RAY DIFFRACTIONr_chiral_restr0.0720.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215951
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021064
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2653
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.278
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5321.53204
X-RAY DIFFRACTIONr_mcbond_other0.121.51292
X-RAY DIFFRACTIONr_mcangle_it0.98325224
X-RAY DIFFRACTIONr_scbond_it1.58131864
X-RAY DIFFRACTIONr_scangle_it2.5634.51750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.511→1.55 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.219 8299 -
Rfree-0 -
obs--99.89 %
Refinement TLS params.Method: refined / Origin x: 15.808 Å / Origin y: 64.846 Å / Origin z: -0.254 Å
111213212223313233
T-0.0097 Å20.0077 Å20.0117 Å2--0.0427 Å20.0047 Å2---0.0316 Å2
L0.3285 °20.0871 °20.1017 °2-0.2855 °2-0.0022 °2--0.3625 °2
S0.0215 Å °-0.0214 Å °0.0048 Å °0.031 Å °-0.0052 Å °0.0274 Å °0.0361 Å °-0.0037 Å °-0.0163 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 575
2X-RAY DIFFRACTION1A588 - 595
3X-RAY DIFFRACTION1A596 - 598

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