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- PDB-3d2a: Structure of 1-17A4, a thermostable mutant of Bacillus subtilis l... -

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Basic information

Entry
Database: PDB / ID: 3d2a
TitleStructure of 1-17A4, 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: 1.73 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


Theoretical massNumber of molelcules
Total (without water)19,4781
Polymers19,4781
Non-polymers00
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.014, 57.958, 82.849
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 19477.912 Da / Num. of mol.: 1 / Mutation: 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.: 143 / 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: 2.34 Å3/Da / Density % sol: 47.5 % / Mosaicity: 1.2 °
Crystal growTemperature: 277 K / Method: small tubes / pH: 10
Details: 2mM glycine-NaOH, pH 10.0, SMALL TUBES, temperature 277K

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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: 1.73→25 Å / Num. obs: 18153 / % possible obs: 92 % / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Χ2: 1.044 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.73-1.792.70.27916200.82585.2
1.79-1.862.90.2221737189.2
1.86-1.952.90.16917341.05489.5
1.95-2.052.90.12517260.99989.1
2.05-2.1830.09317691.00290.1
2.18-2.3530.06618001.01391.8
2.35-2.5830.05818621.04294.3
2.58-2.9630.04719051.07296.4
2.96-3.723.10.03819501.12997.1
3.72-2530.03820501.21396

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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: 1.73→25 Å / FOM work R set: 0.871 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.221 933 4.7 %
Rwork0.192 --
obs-18119 91.7 %
Solvent computationBsol: 61.747 Å2
Displacement parametersBiso mean: 16.212 Å2
Baniso -1Baniso -2Baniso -3
1-1.465 Å20 Å20 Å2
2---0.336 Å20 Å2
3----1.129 Å2
Refinement stepCycle: LAST / Resolution: 1.73→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 143 1500
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it0.00451.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it1.192
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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