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- PDB-4ubj: KINETIC CRYSTALLOGRAPHY OF ALPHA_E7-CARBOXYLESTERSE FROM LUCILLA ... -

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Basic information

Entry
Database: PDB / ID: 4ubj
TitleKINETIC CRYSTALLOGRAPHY OF ALPHA_E7-CARBOXYLESTERSE FROM LUCILLA CUPRINA - ABSORBED X-RAY DOSE 5.55 MGy at 100K
ComponentsE3
KeywordsHYDROLASE / ALPHA/BETA HYDROLASE FOLD / CARBOXYLESTERASE
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJackson, C.J. / Carr, P.D. / Weik, M. / Huber, T. / Meirelles, T. / Correy, G.
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
DepositionAug 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Jun 22, 2016Group: Database references
Revision 1.3Dec 18, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list / reflns_shell
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.Rmerge_I_obs
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6272
Polymers65,4731
Non-polymers1541
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint4 kcal/mol
Surface area22020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.539, 101.073, 222.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-738-

HOH

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Components

#1: Protein E3


Mass: 65472.773 Da / Num. of mol.: 1 / Mutation: M364L, I419F, A472T, I505T, K530E, D554G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucilia cuprina (Australian sheep blowfly)
Gene: LcaE7 / Plasmid: PETMCSIII / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25252
#2: Chemical ChemComp-DPF / DIETHYL HYDROGEN PHOSPHATE


Mass: 154.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O4P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.08 Å3/Da / Density % sol: 40.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 100MM PEG2000, 0.1M MES, PH 4.6, VAPOR DIFFUSION, TEMPERATURE 298K
PH range: 4.6

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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
RadiationMonochromator: CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.3→46.01 Å / Num. obs: 24832 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.146 / Net I/σ(I): 10.4
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.416 / Mean I/σ(I) obs: 1.4 / % possible all: 99.7

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1639)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QWM

4qwm


Resolution: 2.3→46.006 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2336 1262 5.09 %
Rwork0.1699 --
obs0.1732 24795 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→46.006 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 8 208 4775
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084688
X-RAY DIFFRACTIONf_angle_d1.046341
X-RAY DIFFRACTIONf_dihedral_angle_d14.3171759
X-RAY DIFFRACTIONf_chiral_restr0.04677
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.39210.32671330.23642590X-RAY DIFFRACTION100
2.3921-2.5010.30761330.22232542X-RAY DIFFRACTION100
2.501-2.63280.34231300.20992612X-RAY DIFFRACTION100
2.6328-2.79770.23391480.19582590X-RAY DIFFRACTION100
2.7977-3.01370.281350.18822579X-RAY DIFFRACTION100
3.0137-3.31690.23541510.17572597X-RAY DIFFRACTION100
3.3169-3.79670.23271160.15942640X-RAY DIFFRACTION100
3.7967-4.78260.19511570.1432632X-RAY DIFFRACTION100
4.7826-46.01560.21011590.15572751X-RAY DIFFRACTION99

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