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- PDB-5ivd: The alpha-esterase-7 carboxylesterase, E3, from the blowfly Lucil... -

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Basic information

Entry
Database: PDB / ID: 5ivd
TitleThe alpha-esterase-7 carboxylesterase, E3, from the blowfly Lucilia cuprina: apo-enzyme qFit multi-conformer model
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / carboxylesterase / organophosphate / protein dynamics / acetylcholinesterase
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: 1.71 Å
AuthorsCorrey, G.J. / Jackson, C.J.
CitationJournal: Structure / Year: 2016
Title: Mapping the Accessible Conformational Landscape of an Insect Carboxylesterase Using Conformational Ensemble Analysis and Kinetic Crystallography.
Authors: Correy, G.J. / Carr, P.D. / Meirelles, T. / Mabbitt, P.D. / Fraser, N.J. / Weik, M. / Jackson, C.J.
History
DepositionMar 20, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 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 / 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

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Assembly

Deposited unit
A: Carboxylic ester hydrolase


Theoretical massNumber of molelcules
Total (without water)66,3891
Polymers66,3891
Non-polymers00
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.574, 100.472, 221.715
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 66388.836 Da / Num. of mol.: 1
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.: 274 / 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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM sodium acetate pH 4.5, 20% PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393 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: 0.9393 Å / Relative weight: 1
ReflectionResolution: 1.71→42.9 Å / Num. obs: 59116 / % possible obs: 99.86 % / Redundancy: 29 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 19.5
Reflection shellResolution: 1.71→1.74 Å / Redundancy: 28.3 % / Rmerge(I) obs: 3.8 / Mean I/σ(I) obs: 1.1 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FNG

4fng


Resolution: 1.71→42.9 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2303 2999 5.07 %
Rwork0.1776 --
obs0.1802 59116 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 0 274 4831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076823
X-RAY DIFFRACTIONf_angle_d0.9999478
X-RAY DIFFRACTIONf_dihedral_angle_d13.5742660
X-RAY DIFFRACTIONf_chiral_restr0.0421019
X-RAY DIFFRACTIONf_plane_restr0.0051284
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7101-1.73810.49941350.412660X-RAY DIFFRACTION98
1.7381-1.76810.39381370.35922580X-RAY DIFFRACTION100
1.7681-1.80020.3581570.32852693X-RAY DIFFRACTION100
1.8002-1.83490.34931380.29892555X-RAY DIFFRACTION100
1.8349-1.87230.31691510.27192678X-RAY DIFFRACTION100
1.8723-1.9130.30621390.24262622X-RAY DIFFRACTION100
1.913-1.95750.29271330.22142666X-RAY DIFFRACTION100
1.9575-2.00650.27871170.21462693X-RAY DIFFRACTION100
2.0065-2.06070.26431530.2072648X-RAY DIFFRACTION100
2.0607-2.12140.24511110.19892675X-RAY DIFFRACTION100
2.1214-2.18980.25431610.18642621X-RAY DIFFRACTION100
2.1898-2.26810.281360.17862662X-RAY DIFFRACTION100
2.2681-2.35890.24491510.17182646X-RAY DIFFRACTION100
2.3589-2.46630.24151520.17432665X-RAY DIFFRACTION100
2.4663-2.59630.22251490.17022653X-RAY DIFFRACTION100
2.5963-2.75890.24571570.16972688X-RAY DIFFRACTION100
2.7589-2.97190.23641490.18262674X-RAY DIFFRACTION100
2.9719-3.27090.2121420.17342723X-RAY DIFFRACTION100
3.2709-3.7440.1891420.15072718X-RAY DIFFRACTION100
3.744-4.71630.18431440.12842725X-RAY DIFFRACTION100
4.7163-45.77340.191450.15382872X-RAY DIFFRACTION100

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