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- PDB-5c8v: Lucilia cuprina alpha esterase 7: Gly137Asp -

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Basic information

Entry
Database: PDB / ID: 5c8v
TitleLucilia cuprina alpha esterase 7: Gly137Asp
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / Acetylcholinesterase / Animals / Australia / Carboxylesterase / Catalytic Domain / Diptera / Drug Resistance / Genes / Insect / Insecticides / Phosphorylation / Protein Structure / Sheep / Sheep Diseases / Substrate Specificity
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / carboxylic ester hydrolase activity
Similarity search - Function
Carboxylesterase type B, active site / Carboxylesterases type-B serine active site. / Carboxylesterase, type B / Carboxylesterase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsCorrey, G.J. / Mabbitt, P.D. / Jackson, C.J.
CitationJournal: Biochemistry / Year: 2016
Title: Conformational Disorganization within the Active Site of a Recently Evolved Organophosphate Hydrolase Limits Its Catalytic Efficiency.
Authors: Mabbitt, P.D. / Correy, G.J. / Meirelles, T. / Fraser, N.J. / Coote, M.L. / Jackson, C.J.
History
DepositionJun 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)65,4871
Polymers65,4871
Non-polymers00
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.674, 102.583, 225.476
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-807-

HOH

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 65486.797 Da / Num. of mol.: 1
Mutation: D83A, G137D, M364L, I419F, A472T, I505T, K530E, D554G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly)
Gene: LcaE7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q25252, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 100 mM sodium-acetate (pH 4.6) and 20% PEG 2K MME / PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.8726 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 20, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.01→56.37 Å / Num. obs: 44051 / % possible obs: 95.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 7.7
Reflection shellResolution: 2.01→2.06 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.906 / Mean I/σ(I) obs: 1.4 / % possible all: 98.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
XSCALEdata scaling
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNG

4fng


Resolution: 2.01→56.37 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.929 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24451 1867 5 %RANDOM
Rwork0.18473 ---
obs0.18765 35283 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.01→56.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4561 0 0 208 4769
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194706
X-RAY DIFFRACTIONr_bond_other_d0.0010.024420
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9556373
X-RAY DIFFRACTIONr_angle_other_deg0.877310210
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5215571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.36924.305223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07115829
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5181525
X-RAY DIFFRACTIONr_chiral_restr0.1040.2679
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021094
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_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9432.5372278
X-RAY DIFFRACTIONr_mcbond_other1.9442.5372277
X-RAY DIFFRACTIONr_mcangle_it2.8893.7972851
X-RAY DIFFRACTIONr_mcangle_other2.8893.7972852
X-RAY DIFFRACTIONr_scbond_it2.5322.832428
X-RAY DIFFRACTIONr_scbond_other2.5322.832428
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.934.1253522
X-RAY DIFFRACTIONr_long_range_B_refined5.19320.3335508
X-RAY DIFFRACTIONr_long_range_B_other5.16220.2935447
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 133 -
Rwork0.302 2644 -
obs--97.85 %

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