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

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Basic information

Entry
Database: PDB / ID: 4ubi
TitleKINETIC CRYSTALLOGRAPHY OF ALPHA_E7-CARBOXYLESTERSE FROM LUCILLA CUPRINA - ABSORBED X-RAY DOSE 3.70 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: 2.24 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 area21950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.533, 101.044, 222.282
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-739-

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

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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: 2.24→45.99 Å / Num. obs: 26772 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 37.93 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 10.5
Reflection shellResolution: 2.24→2.31 Å / Redundancy: 6.3 % / Rmerge(I) obs: 1.519 / Mean I/σ(I) obs: 1.3 / Rejects: 0 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX(phenix.refine: dev_1639)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QWM

4qwm


Resolution: 2.24→45.99 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1352 5.06 %
Rwork0.175 25385 -
obs0.178 26737 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.83 Å2 / Biso mean: 43.1293 Å2 / Biso min: 23.88 Å2
Refinement stepCycle: final / Resolution: 2.24→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 8 208 4775
Biso mean--40.69 43.69 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084688
X-RAY DIFFRACTIONf_angle_d1.0236341
X-RAY DIFFRACTIONf_chiral_restr0.041677
X-RAY DIFFRACTIONf_plane_restr0.005817
X-RAY DIFFRACTIONf_dihedral_angle_d14.2681759
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.24-2.32010.31121200.22262494261499
2.3201-2.4130.3071270.229425132640100
2.413-2.52280.32371350.218724922627100
2.5228-2.65580.29741190.210225342653100
2.6558-2.82210.25691530.205524982651100
2.8221-3.040.26331310.200925482679100
3.04-3.34580.28071420.183425122654100
3.3458-3.82980.21161200.163925512671100
3.8298-4.82430.18421480.14272575272399
4.8243-46.00270.19651570.15592668282599

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