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- PDB-5ikx: Crystal structure of the alpha-esterase-7 carboxyl esterase (dime... -

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Basic information

Entry
Database: PDB / ID: 5ikx
TitleCrystal structure of the alpha-esterase-7 carboxyl esterase (dimer), E3, from Lucilia cuprina
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / organophosphate / carboxylesterase / oligermerization
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: 2.19 Å
AuthorsJackson, C. / Fraser, N.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Evolution of Protein Quaternary Structure in Response to Selective Pressure for Increased Thermostability.
Authors: Fraser, N.J. / Liu, J.W. / Mabbitt, P.D. / Correy, G.J. / Coppin, C.W. / Lethier, M. / Perugini, M.A. / Murphy, J.M. / Oakeshott, J.G. / Weik, M. / Jackson, C.J.
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionJun 22, 2016ID: 4FG5
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _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

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Assembly

Deposited unit
A: Carboxylic ester hydrolase
B: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)132,7782
Polymers132,7782
Non-polymers00
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1020 Å2
ΔGint1 kcal/mol
Surface area44210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.767, 108.956, 92.172
Angle α, β, γ (deg.)90.00, 90.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 66388.836 Da / Num. of mol.: 2
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.: 376 / 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: 2.37 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 100 mM MES, 20% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.82655 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82655 Å / Relative weight: 1
ReflectionResolution: 2.19→46.9 Å / Num. obs: 62125 / % possible obs: 97.9 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.7
Reflection shellResolution: 2.19→2.31 Å / Rmerge(I) obs: 0.439

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNG

4fng


Resolution: 2.19→47.06 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 11.304 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.209 3276 5.3 %RANDOM
Rwork0.171 ---
obs0.173 58544 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.72 Å20 Å2-15.41 Å2
2--14.12 Å20 Å2
3----25.84 Å2
Refinement stepCycle: LAST / Resolution: 2.19→47.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9140 0 0 376 9516
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029372
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.95512685
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.88751136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56324.324444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.695151634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8161549
X-RAY DIFFRACTIONr_chiral_restr0.0820.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217153
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellHighest resolution: 2.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 172 -
Rwork0.237 3419 -
obs--77.73 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2579-0.1835-0.2810.19360.341.2130.02560.06390.02840.0397-0.06660.02040.20670.05740.0410.13350.05330.11830.1499-0.03020.225213.815-4.735-5.664
20.38090.1415-0.22660.25880.18020.4881-0.04720.0114-0.02160.02290.04830.01040.04820.0223-0.0010.12110.01980.09580.15210.00160.23034.0062.92511.019
30.8219-0.1377-0.55860.28430.42470.82470.11670.10490.0369-0.0914-0.0557-0.0182-0.2097-0.0875-0.0610.17250.03020.1150.10250.01390.19091.922.848-0.577
40.1943-0.3038-0.39440.94270.70090.9989-0.056-0.02980.0077-0.07180.03820.0008-0.06180.02170.01790.19740.06110.07380.15610.02930.20715.043.552-51.986
50.355-0.05420.08590.03730.0030.7911-0.06590.0231-0.0125-0.00710.0523-0.0018-0.02770.05540.01360.0843-0.00930.11410.1580.0070.230324.435-3.974-34.947
60.31-0.2460.14670.3414-0.03310.8386-0.02490.0239-0.0021-0.07470.02320.0150.23230.12150.00170.23880.030.09260.1173-0.00760.195226.329-24.127-46.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 66
2X-RAY DIFFRACTION2A67 - 347
3X-RAY DIFFRACTION3A348 - 570
4X-RAY DIFFRACTION4B2 - 66
5X-RAY DIFFRACTION5B67 - 347
6X-RAY DIFFRACTION6B348 - 570

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