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- PDB-5ct4: Wild-type Bacillus subtilis lipase A with 5% [BMIM][Cl] -

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Basic information

Entry
Database: PDB / ID: 5ct4
TitleWild-type Bacillus subtilis lipase A with 5% [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: 1.49 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: Esterase
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2268
Polymers38,6242
Non-polymers6026
Water9,026501
1
A: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7225
Polymers19,3121
Non-polymers4104
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Esterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5043
Polymers19,3121
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.440, 83.160, 95.820
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: 19311.758 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C8H15N2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 501 / 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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 35 % PEG 3350, 20 mM NaSO4, 0.1M ethanolamine, 10mM ZnCl2, pH 9.5
Temp details: Room temp

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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: 1.49→39.4 Å / Num. obs: 52595 / % possible obs: 99.4 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 16.9
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 7.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
iMOSFLMdata reduction
RefinementResolution: 1.49→39.4 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / Phase error: 13.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1564 2000 3.81 %
Rwork0.1262 --
obs0.1274 52536 99.4 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.006 Å2 / ksol: 0.33 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.4721 Å20 Å2-0 Å2
2--1.0597 Å20 Å2
3----0.7417 Å2
Refinement stepCycle: LAST / Resolution: 1.49→39.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2711 0 36 501 3248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092815
X-RAY DIFFRACTIONf_angle_d1.2033817
X-RAY DIFFRACTIONf_dihedral_angle_d12.5471007
X-RAY DIFFRACTIONf_chiral_restr0.069422
X-RAY DIFFRACTIONf_plane_restr0.007492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.485-1.52210.21681340.16443382X-RAY DIFFRACTION94
1.5221-1.56330.17081410.13383569X-RAY DIFFRACTION100
1.5633-1.60930.17081410.11323558X-RAY DIFFRACTION100
1.6093-1.66120.15991420.10753587X-RAY DIFFRACTION100
1.6612-1.72060.15851410.10583575X-RAY DIFFRACTION100
1.7206-1.78950.14691430.10333606X-RAY DIFFRACTION100
1.7895-1.8710.14011420.10883582X-RAY DIFFRACTION100
1.871-1.96960.16381420.11833616X-RAY DIFFRACTION100
1.9696-2.0930.14951430.12193611X-RAY DIFFRACTION100
2.093-2.25460.15521460.11563647X-RAY DIFFRACTION100
2.2546-2.48140.16551440.11453642X-RAY DIFFRACTION100
2.4814-2.84030.14671440.12643661X-RAY DIFFRACTION100
2.8403-3.5780.16671470.13193692X-RAY DIFFRACTION100
3.578-36.48230.14421500.15033808X-RAY DIFFRACTION98

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