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- PDB-5cta: G158E/K44E/R57E/Y49E Bacillus subtilis lipase A with 10% [BMIM][Cl] -

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Basic information

Entry
Database: PDB / ID: 5cta
TitleG158E/K44E/R57E/Y49E Bacillus subtilis lipase A with 10% [BMIM][Cl]
ComponentsEsterase
KeywordsHYDROLASE
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region
Similarity search - Function
Lipase EstA/Esterase EstB / Lipase (class 2) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1-butyl-3-methyl-1H-imidazol-3-ium / Lipase / Lipase EstA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.24 Å
AuthorsNordwald, E.M. / Plaks, J.G. / Snell, J.R. / Sousa, M.C. / Kaar, J.L.
CitationJournal: Chembiochem / Year: 2015
Title: Crystallographic Investigation of Imidazolium Ionic Liquid Effects on Enzyme Structure.
Authors: Nordwald, E.M. / Plaks, J.G. / Snell, J.R. / Sousa, M.C. / Kaar, J.L.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4963
Polymers19,3221
Non-polymers1752
Water6,413356
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.210, 55.950, 64.420
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Esterase / Lipase / Lipase A


Mass: 19321.613 Da / Num. of mol.: 1 / Mutation: K75E, Y80E, R88E, G189E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA, QX56_01625 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: I6V559, UniProt: P37957*PLUS, triacylglycerol lipase
#2: Chemical ChemComp-BM0 / 1-butyl-3-methyl-1H-imidazol-3-ium / 1-butyl-3-methylimidazolium


Mass: 139.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15N2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 35 % PEG 3350, 20 mM NaSO4, 0.1M ethanolamine, 10mM ZnCl2, pH 9.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.24→27.9 Å / Num. obs: 45856 / % possible obs: 92.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 18.2
Reflection shellResolution: 1.24→1.31 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.072 / Mean I/σ(I) obs: 12.5 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
iMOSFLMdata reduction
RefinementResolution: 1.24→20.048 Å / SU ML: 0.08 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 7.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1349 2000 4.37 %
Rwork0.1089 --
obs0.11 45803 91.54 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.818 Å2 / ksol: 0.434 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5492 Å20 Å20 Å2
2--0.071 Å2-0 Å2
3---0.4755 Å2
Refinement stepCycle: LAST / Resolution: 1.24→20.048 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 11 356 1718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091398
X-RAY DIFFRACTIONf_angle_d1.2921899
X-RAY DIFFRACTIONf_dihedral_angle_d11.759502
X-RAY DIFFRACTIONf_chiral_restr0.072213
X-RAY DIFFRACTIONf_plane_restr0.008248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.24-1.2710.11651500.09153279X-RAY DIFFRACTION98
1.271-1.30540.10611500.08693308X-RAY DIFFRACTION98
1.3054-1.34380.11431540.08073342X-RAY DIFFRACTION98
1.3438-1.38710.10041510.08233319X-RAY DIFFRACTION99
1.3871-1.43670.10451530.08013353X-RAY DIFFRACTION99
1.4367-1.49420.10431530.0833349X-RAY DIFFRACTION99
1.4942-1.56220.11711550.08283386X-RAY DIFFRACTION99
1.5622-1.64450.12081540.08613385X-RAY DIFFRACTION99
1.6445-1.74750.10681550.08843387X-RAY DIFFRACTION99
1.7475-1.88230.11421540.09743388X-RAY DIFFRACTION100
1.8823-2.07160.12781550.10393373X-RAY DIFFRACTION98
2.0716-2.37090.14951440.11883151X-RAY DIFFRACTION91
2.3709-2.98560.19061200.1612636X-RAY DIFFRACTION76
2.9856-20.05010.3733520.30681147X-RAY DIFFRACTION32

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