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- PDB-5w1u: Culex quinquefasciatus carboxylesterase B2 -

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Basic information

Entry
Database: PDB / ID: 5w1u
TitleCulex quinquefasciatus carboxylesterase B2
ComponentsCarboxylic ester hydrolase
KeywordsHYDROLASE / Carboxylesterase / alpha/beta hydrolase
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
MALONATE ION / Carboxylic ester hydrolase
Similarity search - Component
Biological speciesCulex quinquefasciatus (southern house mosquito)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHopkins, D.H. / Jackson, C.J.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian Research Council (ARC) Australia
CitationJournal: Biochemistry / Year: 2017
Title: Structure of an Insecticide Sequestering Carboxylesterase from the Disease Vector Culex quinquefasciatus: What Makes an Enzyme a Good Insecticide Sponge?
Authors: Hopkins, D.H. / Fraser, N.J. / Mabbitt, P.D. / Carr, P.D. / Oakeshott, J.G. / Jackson, C.J.
History
DepositionJun 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2076
Polymers121,5262
Non-polymers6814
Water4,684260
1
A: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1033
Polymers60,7631
Non-polymers3402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carboxylic ester hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1033
Polymers60,7631
Non-polymers3402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.070, 125.070, 168.811
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Carboxylic ester hydrolase


Mass: 60763.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Culex quinquefasciatus (southern house mosquito)
Production host: Escherichia coli (E. coli)
References: UniProt: Q23734, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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: 3.14 Å3/Da / Density % sol: 60.84 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 1.6 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.5→91.16 Å / Num. obs: 53392 / % possible obs: 100 % / Redundancy: 10.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.051 / Net I/σ(I): 11.7
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 10.9 % / Rmerge(I) obs: 1.226 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4561 / CC1/2: 0.578 / Rpim(I) all: 0.387 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.581 Å / SU ML: 0.42 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 26.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2698 2599 4.87 %
Rwork0.1947 --
obs0.1984 53336 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→45.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8489 0 44 260 8793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168741
X-RAY DIFFRACTIONf_angle_d1.64611842
X-RAY DIFFRACTIONf_dihedral_angle_d17.6923254
X-RAY DIFFRACTIONf_chiral_restr0.0641261
X-RAY DIFFRACTIONf_plane_restr0.0081548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.54550.37881250.30242629X-RAY DIFFRACTION100
2.5455-2.59440.36481520.28572622X-RAY DIFFRACTION100
2.5944-2.64740.38091190.27372633X-RAY DIFFRACTION100
2.6474-2.70490.34121150.25992665X-RAY DIFFRACTION100
2.7049-2.76780.32431390.26172660X-RAY DIFFRACTION100
2.7678-2.83710.36081310.25032650X-RAY DIFFRACTION100
2.8371-2.91380.33621490.25012628X-RAY DIFFRACTION100
2.9138-2.99950.31281510.24522630X-RAY DIFFRACTION100
2.9995-3.09630.33171360.24362652X-RAY DIFFRACTION100
3.0963-3.20690.31771160.22562668X-RAY DIFFRACTION100
3.2069-3.33530.27751320.21592647X-RAY DIFFRACTION100
3.3353-3.4870.2993860.20712722X-RAY DIFFRACTION100
3.487-3.67080.29251310.19472673X-RAY DIFFRACTION100
3.6708-3.90060.22581670.17692630X-RAY DIFFRACTION100
3.9006-4.20160.24421830.16532644X-RAY DIFFRACTION100
4.2016-4.62410.24651390.15472691X-RAY DIFFRACTION100
4.6241-5.29230.21361320.14612717X-RAY DIFFRACTION100
5.2923-6.66450.2291370.15132732X-RAY DIFFRACTION100
6.6645-45.58860.20971590.14912844X-RAY DIFFRACTION100

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