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- PDB-5ct5: Wild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] -

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Basic information

Entry
Database: PDB / ID: 5ct5
TitleWild-type Bacillus subtilis lipase A with 10% [BMIM][Cl]
ComponentsWild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] chain A
KeywordsHYDROLASE / Wild-type / ionic liquid / lipase
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 / MOLECULAR REPLACEMENT / Resolution: 1.747 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 23, 2016Group: Source and taxonomy
Revision 1.3Sep 27, 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 / database_2 / pdbx_initial_refinement_model / 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: Wild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] chain A
B: Wild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1737
Polymers38,6242
Non-polymers5495
Water7,080393
1
A: Wild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5824
Polymers19,3121
Non-polymers2713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Wild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5903
Polymers19,3121
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.270, 82.780, 95.500
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 Wild-type Bacillus subtilis lipase A with 10% [BMIM][Cl] chain A / Lipase / Lipase A


Mass: 19311.758 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: I6V559, UniProt: P37957*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BM0 / 1-butyl-3-methyl-1H-imidazol-3-ium / 1-butyl-3-methylimidazolium


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


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


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.01 Å3/Da / Density % sol: 38.79 %
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: 1.747→41.4 Å / Num. obs: 32167 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 12.5
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6.3 / % possible all: 98.7

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
iMOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I6W

1i6w


Resolution: 1.747→41.39 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1731 2000 6.23 %
Rwork0.1287 --
obs0.1315 32127 99.18 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.14 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6165 Å20 Å2-0 Å2
2--1.1922 Å20 Å2
3----0.2514 Å2
Refinement stepCycle: LAST / Resolution: 1.747→41.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 36 393 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112806
X-RAY DIFFRACTIONf_angle_d1.3753799
X-RAY DIFFRACTIONf_dihedral_angle_d13.171999
X-RAY DIFFRACTIONf_chiral_restr0.087418
X-RAY DIFFRACTIONf_plane_restr0.007491
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.747-1.79070.28981390.1712092X-RAY DIFFRACTION97
1.7907-1.83910.19441420.13632136X-RAY DIFFRACTION99
1.8391-1.89330.20451390.12072105X-RAY DIFFRACTION100
1.8933-1.95440.18731420.11542144X-RAY DIFFRACTION100
1.9544-2.02420.17461420.10192117X-RAY DIFFRACTION100
2.0242-2.10530.17651430.10612153X-RAY DIFFRACTION100
2.1053-2.20110.15011400.10362135X-RAY DIFFRACTION100
2.2011-2.31710.1621450.09912162X-RAY DIFFRACTION100
2.3171-2.46230.16421420.11352155X-RAY DIFFRACTION100
2.4623-2.65230.15971430.11782156X-RAY DIFFRACTION100
2.6523-2.91920.17421440.13072152X-RAY DIFFRACTION100
2.9192-3.34140.17811440.14012181X-RAY DIFFRACTION99
3.3414-4.20920.16541450.13392181X-RAY DIFFRACTION98
4.2092-41.40160.16061500.16732258X-RAY DIFFRACTION97

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