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- PDB-3d2b: Structure of 2D9, a thermostable mutant of Bacillus subtilis lipa... -

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Basic information

Entry
Database: PDB / ID: 3d2b
TitleStructure of 2D9, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution
ComponentsLipase
KeywordsHYDROLASE / lipase / alpha/beta hydrolase / stability / directed evolution / Lipid degradation / Secreted
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
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSankaranarayanan, R. / Kamal, M.Z.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Thermostable Bacillus subtilis lipases: in vitro evolution and structural insight
Authors: Ahmad, S. / Kamal, M.Z. / Sankaranarayanan, R. / Rao, N.M.
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase


Theoretical massNumber of molelcules
Total (without water)38,9342
Polymers38,9342
Non-polymers00
Water5,639313
1
A: Lipase


Theoretical massNumber of molelcules
Total (without water)19,4671
Polymers19,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipase


Theoretical massNumber of molelcules
Total (without water)19,4671
Polymers19,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.203, 117.399, 117.555
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 19466.889 Da / Num. of mol.: 2 / Mutation: F17S, N89Y, L114P, A132D, I157M, N166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: lipA, lip, BSU02700 / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P37957, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O

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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: 3.33 Å3/Da / Density % sol: 63.09 % / Mosaicity: 0.593 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 100mM Ethanolamine buffe, 10mM Sodium sulfate, pH 9.5, vapour diffusion, sitting drop, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 36223 / % possible obs: 94.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.066 / Χ2: 0.561 / Net I/σ(I): 10.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-2.023.30.27735390.51593.2
2.02-2.13.40.21336970.50697.7
2.1-2.23.50.16437420.50898.3
2.2-2.313.50.13837210.52197.7
2.31-2.463.60.11336830.52696.7
2.46-2.653.60.0936540.53696
2.65-2.913.70.0736290.57394.3
2.91-3.333.80.04635700.55692.7
3.33-4.23.90.03235110.71690.4
4.2-253.90.02634770.62586.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→25 Å / FOM work R set: 0.885 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.21 1801 4.7 %
Rwork0.184 --
obs-36163 94.5 %
Solvent computationBsol: 41.541 Å2
Displacement parametersBiso mean: 15.955 Å2
Baniso -1Baniso -2Baniso -3
1-3.928 Å20 Å20 Å2
2--2.652 Å20 Å2
3----6.58 Å2
Refinement stepCycle: LAST / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2712 0 0 313 3025
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.0051.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it1.172
X-RAY DIFFRACTIONc_scangle_it2.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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