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- PDB-5ct6: Wild-type Bacillus subtilis lipase A with 20% [BMIM][Cl] -

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Basic information

Entry
Database: PDB / ID: 5ct6
TitleWild-type Bacillus subtilis lipase A with 20% [BMIM][Cl]
ComponentsLipase EstA
KeywordsHYDROLASE
Function / homology
Function and homology information


lipase activity / triacylglycerol lipase / triglyceride 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 EstA
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.902 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

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Assembly

Deposited unit
A: Lipase EstA
B: Lipase EstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,84413
Polymers38,6242
Non-polymers1,22011
Water4,179232
1
A: Lipase EstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0437
Polymers19,3121
Non-polymers7326
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase EstA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8006
Polymers19,3121
Non-polymers4895
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-33 kcal/mol
Surface area14430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.901, 74.901, 112.351
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Lipase EstA / Lipase A / Triacylglycerol lipase


Mass: 19311.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: estA, lip, lipA, BSU02700 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-BM0 / 1-butyl-3-methyl-1H-imidazol-3-ium / 1-butyl-3-methylimidazolium / C4mim


Mass: 139.218 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H15N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.05 Å3/Da / Density % sol: 40.11 %
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: 1.9→48 Å / Num. obs: 25866 / % possible obs: 100 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 14.5
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
iMOSFLMdata reduction
RefinementResolution: 1.902→47.907 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2292 1997 7.74 %
Rwork0.1905 --
obs0.1934 25788 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.139 Å2 / ksol: 0.331 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2042 Å20 Å20 Å2
2--2.2042 Å2-0 Å2
3----4.2288 Å2
Refinement stepCycle: LAST / Resolution: 1.902→47.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2702 0 83 232 3017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112887
X-RAY DIFFRACTIONf_angle_d1.1723897
X-RAY DIFFRACTIONf_dihedral_angle_d14.7911028
X-RAY DIFFRACTIONf_chiral_restr0.078419
X-RAY DIFFRACTIONf_plane_restr0.005501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9018-1.94940.41091380.36091643X-RAY DIFFRACTION100
1.9494-2.00210.30451420.26081684X-RAY DIFFRACTION100
2.0021-2.0610.27411390.24151672X-RAY DIFFRACTION100
2.061-2.12750.23821400.19991662X-RAY DIFFRACTION100
2.1275-2.20350.19551430.19621692X-RAY DIFFRACTION100
2.2035-2.29180.2541380.1861654X-RAY DIFFRACTION100
2.2918-2.39610.21081420.18451682X-RAY DIFFRACTION100
2.3961-2.52240.22751420.17491689X-RAY DIFFRACTION100
2.5224-2.68040.22311410.18231692X-RAY DIFFRACTION100
2.6804-2.88730.20441450.17661709X-RAY DIFFRACTION100
2.8873-3.17780.23791410.18331688X-RAY DIFFRACTION100
3.1778-3.63760.22141470.1821736X-RAY DIFFRACTION100
3.6376-4.58240.20231450.15421737X-RAY DIFFRACTION100
4.5824-47.9220.22861540.20751851X-RAY DIFFRACTION99

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