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

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Basic information

Entry
Database: PDB / ID: 4ubn
TitleKINETIC CRYSTALLOGRAPHY OF ALPHA_E7-CARBOXYLESTERSE FROM LUCILLA CUPRINA - ABSORBED X-RAY DOSE 1.85 MGy TEMP 150K
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: 2.02 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 1.3Nov 8, 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint4 kcal/mol
Surface area22060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.303, 101.351, 222.991
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 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)
Strain: LS2 / 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.: 203 / 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: 2.08 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: 150 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: 2.02→46.13 Å / Num. obs: 36959 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 9.2
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 1.8 / % possible all: 91

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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: 2.02→46.13 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2584 1871 5.07 %
Rwork0.2042 --
obs0.207 36905 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.02→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4559 0 8 203 4770
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074688
X-RAY DIFFRACTIONf_angle_d1.0476341
X-RAY DIFFRACTIONf_dihedral_angle_d13.7171759
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 (%)
2.02-2.07460.38241370.30692428X-RAY DIFFRACTION91
2.0746-2.13570.35821380.27722646X-RAY DIFFRACTION99
2.1357-2.20460.30471260.25272677X-RAY DIFFRACTION100
2.2046-2.28340.3191560.23922670X-RAY DIFFRACTION100
2.2834-2.37480.29411320.23162713X-RAY DIFFRACTION100
2.3748-2.48290.32681330.22832711X-RAY DIFFRACTION100
2.4829-2.61380.3191410.22572696X-RAY DIFFRACTION100
2.6138-2.77750.27171520.22082685X-RAY DIFFRACTION100
2.7775-2.9920.29581470.22912720X-RAY DIFFRACTION100
2.992-3.2930.24671520.21592720X-RAY DIFFRACTION100
3.293-3.76930.24181290.18822764X-RAY DIFFRACTION100
3.7693-4.74810.2031600.16172733X-RAY DIFFRACTION100
4.7481-46.1460.20541680.16362871X-RAY DIFFRACTION100

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