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- PDB-2o7v: Carboxylesterase AeCXE1 from Actinidia eriantha covalently inhibi... -

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Basic information

Entry
Database: PDB / ID: 2o7v
TitleCarboxylesterase AeCXE1 from Actinidia eriantha covalently inhibited by paraoxon
ComponentsCXE carboxylesterase
KeywordsHYDROLASE / carboxylesterase / Actinidia eriantha / AeCXE1 / alpha/beta hydrolase / paraoxon / insecticide
Function / homology
Function and homology information


carboxylesterase / carboxylesterase activity
Similarity search - Function
Lipase, GDXG, putative histidine active site / Lipolytic enzymes "G-D-X-G" family, putative histidine active site. / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DIETHYL PHOSPHONATE / Carboxylesterase 1
Similarity search - Component
Biological speciesActinidia eriantha (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIleperuma, N.R. / Marshall, S.D. / Squire, C.J. / Baker, H.M. / Oakeshott, J.G. / Russell, R.J. / Plummer, K.M. / Newcomb, R.D. / Baker, E.N.
CitationJournal: Biochemistry / Year: 2007
Title: High-Resolution Crystal Structure of Plant Carboxylesterase AeCXE1, from Actinidia eriantha, and Its Complex with a High-Affinity Inhibitor Paraoxon.
Authors: Ileperuma, N.R. / Marshall, S.D. / Squire, C.J. / Baker, H.M. / Oakeshott, J.G. / Russell, R.J. / Plummer, K.M. / Newcomb, R.D. / Baker, E.N.
History
DepositionDec 11, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CXE carboxylesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5902
Polymers37,4521
Non-polymers1381
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.078, 53.908, 42.366
Angle α, β, γ (deg.)90.00, 102.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CXE carboxylesterase


Mass: 37451.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinidia eriantha (plant) / Gene: CXE1 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q0ZPV7, carboxylesterase
#2: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 21% mPEG 5000, 0.2 M malic/KOH pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 8, 2006 / Details: osmic
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→33.5 Å / Num. all: 14481 / Num. obs: 14481 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.097 / Net I/σ(I): 14.8
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2000 / Rsym value: 0.426 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 207R

207r


Resolution: 2.3→33.5 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.905 / SU B: 7.092 / SU ML: 0.172 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.356 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24868 723 5 %RANDOM
Rwork0.18658 ---
all0.18963 13758 --
obs0.18963 13758 93.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.443 Å2
Baniso -1Baniso -2Baniso -3
1--2.11 Å20 Å2-0.32 Å2
2--0.43 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 8 58 2469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0222471
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8831.9733353
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9525303
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.29723.271107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.24515400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6731516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2373
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021863
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21032
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21621
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0191.51579
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67522463
X-RAY DIFFRACTIONr_scbond_it2.54831020
X-RAY DIFFRACTIONr_scangle_it3.854.5890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 56 -
Rwork0.242 964 -
obs--87.86 %

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