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

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Basic information

Entry
Database: PDB / ID: 5ivk
TitleThe alpha-esterase-7 carboxylesterase, E3, from the blowfly Lucilia cuprina: phosphorylated-enzyme ensemble refinement
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
DIETHYL HYDROGEN PHOSPHATE / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesLucilia cuprina (Australian sheep blowfly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.53 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 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5872
Polymers66,4331
Non-polymers1541
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.816, 101.254, 225.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Number of models43
Components on special symmetry positions
IDModelComponents
11A-829-

HOH

22A-1025-

HOH

33A-1004-

HOH

43A-1035-

HOH

54A-1020-

HOH

64A-1039-

HOH

75A-1022-

HOH

85A-1057-

HOH

96A-1015-

HOH

106A-1028-

HOH

117A-756-

HOH

128A-962-

HOH

139A-766-

HOH

1410A-836-

HOH

1511A-960-

HOH

1611A-1034-

HOH

1712A-752-

HOH

1813A-968-

HOH

1914A-769-

HOH

2017A-783-

HOH

2118A-742-

HOH

2219A-716-

HOH

2319A-1018-

HOH

2420A-779-

HOH

2520A-1088-

HOH

2621A-955-

HOH

2722A-838-

HOH

2823A-752-

HOH

2924A-912-

HOH

3025A-1004-

HOH

3126A-727-

HOH

3227A-879-

HOH

3328A-833-

HOH

3429A-749-

HOH

3530A-943-

HOH

3631A-824-

HOH

3732A-762-

HOH

3833A-887-

HOH

3938A-925-

HOH

4039A-966-

HOH

4140A-792-

HOH

4241A-969-

HOH

4342A-909-

HOH

4443A-737-

HOH

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 66432.844 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: Chemical ChemComp-DPF / DIETHYL HYDROGEN PHOSPHATE


Mass: 154.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H11O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.26 Å3/Da / Density % sol: 45.62 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM sodium acetate pH 4.5, PEG 2K MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8266 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: 0.8266 Å / Relative weight: 1
ReflectionResolution: 1.53→42 Å / Num. obs: 89882 / % possible obs: 100 % / Redundancy: 12.7 % / Net I/σ(I): 11.6
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 12 % / Rmerge(I) obs: 1.79 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 1.53→42.01 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.81
RfactorNum. reflection% reflection
Rfree0.22 4499 5.01 %
Rwork0.181 --
obs0.183 89888 100 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.53→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4557 0 8 399 4964
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.013
X-RAY DIFFRACTIONf_angle_d1.332
X-RAY DIFFRACTIONf_dihedral_angle_d17.88
X-RAY DIFFRACTIONf_chiral_restr0.061
X-RAY DIFFRACTIONf_plane_restr0.009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.53-1.54740.31891370.29182821X-RAY DIFFRACTION100
1.5474-1.56560.30881390.28312819X-RAY DIFFRACTION100
1.5656-1.58470.31171370.26852823X-RAY DIFFRACTION100
1.5847-1.60480.29571540.25072799X-RAY DIFFRACTION100
1.6048-1.62590.31341520.24222864X-RAY DIFFRACTION100
1.6259-1.64810.28421500.23042764X-RAY DIFFRACTION100
1.6481-1.67170.28761560.22512852X-RAY DIFFRACTION100
1.6717-1.69660.29421620.22352749X-RAY DIFFRACTION100
1.6966-1.72320.26491590.21412887X-RAY DIFFRACTION100
1.7232-1.75140.26411540.20082759X-RAY DIFFRACTION100
1.7514-1.78160.2541600.19342856X-RAY DIFFRACTION100
1.7816-1.8140.24871670.19612764X-RAY DIFFRACTION100
1.814-1.84890.24831560.18932848X-RAY DIFFRACTION100
1.8489-1.88660.23081490.19842800X-RAY DIFFRACTION100
1.8866-1.92770.28491340.19882825X-RAY DIFFRACTION100
1.9277-1.97250.20431440.19042875X-RAY DIFFRACTION100
1.9725-2.02180.2441780.18622801X-RAY DIFFRACTION100
2.0218-2.07650.24011460.18032818X-RAY DIFFRACTION100
2.0765-2.13760.21731380.18352854X-RAY DIFFRACTION100
2.1376-2.20660.23261300.17882866X-RAY DIFFRACTION100
2.2066-2.28540.23971460.18242845X-RAY DIFFRACTION100
2.2854-2.37690.2081430.18262884X-RAY DIFFRACTION100
2.3769-2.48510.2621480.17742846X-RAY DIFFRACTION100
2.4851-2.61610.20361590.17552841X-RAY DIFFRACTION100
2.6161-2.780.19381440.16952856X-RAY DIFFRACTION100
2.78-2.99460.21481440.17382908X-RAY DIFFRACTION100
2.9946-3.29580.22781480.17822877X-RAY DIFFRACTION100
3.2958-3.77250.19081370.16892921X-RAY DIFFRACTION100
3.7725-4.75190.15961540.14832938X-RAY DIFFRACTION100
4.7519-42.0250.17421740.15073029X-RAY DIFFRACTION100

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