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- PDB-3qmm: Structure of 6B, a thermostable mutant of Bacillus subtilis lipas... -

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Basic information

Entry
Database: PDB / ID: 3qmm
TitleStructure of 6B, a thermostable mutant of Bacillus subtilis lipase obtained through directed evolution
ComponentsLipase estA
KeywordsHYDROLASE / lipase / alpha/beta hydrolase / stability / directed evolution
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: 1.89 Å
AuthorsSankaranarayanan, R. / Kamal, M.Z.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: In vitro evolved non-aggregating and thermostable lipase: structural and thermodynamic investigation
Authors: Kamal, M.Z. / Ahmad, S. / Molugu, T.R. / Vijayalakshmi, A. / Deshmukh, M.V. / Sankaranarayanan, R. / Rao, N.M.
History
DepositionFeb 4, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase estA
B: Lipase estA


Theoretical massNumber of molelcules
Total (without water)39,1462
Polymers39,1462
Non-polymers00
Water4,540252
1
A: Lipase estA


Theoretical massNumber of molelcules
Total (without water)19,5731
Polymers19,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipase estA


Theoretical massNumber of molelcules
Total (without water)19,5731
Polymers19,5731
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.481, 55.206, 137.064
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 estA / Lipase A / Triacylglycerol lipase


Mass: 19572.834 Da / Num. of mol.: 2
Mutation: A15S,F17S,A20E,N89Y,G111D,L114P,A132D,M134E,M137P,I157M,S163P,N166Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: estA / 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.: 252 / 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: 1.81 Å3/Da / Density % sol: 32.09 % / Mosaicity: 0.507 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M sodium malonate(pH 7.0), 20%(w/v) PEG3350, 25%(w/v) PEG 1500, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 29, 2009 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.89→25 Å / Num. obs: 23336 / % possible obs: 98.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.043 / Χ2: 0.961 / Net I/σ(I): 24.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.89-1.963.60.09920680.674189.1
1.96-2.043.80.08422780.699199.3
2.04-2.133.80.07123220.714199.7
2.13-2.243.80.05923290.855199.8
2.24-2.383.80.05523300.8391100
2.38-2.563.80.0523260.8471100
2.56-2.823.80.04523561.0311100
2.82-3.233.90.03923671.229199.9
3.23-4.073.90.03524131.211100
4.07-253.70.03725471.399199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 0.445 / Cor.coef. Fo:Fc: 0.58
Highest resolutionLowest resolution
Rotation4 Å24.55 Å
Translation4 Å24.55 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1I6W(chain A)

1i6w


Resolution: 1.89→25 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8323 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2446 1206 5.1 %
Rwork0.1942 --
obs-23029 99.1 %
Solvent computationBsol: 30.972 Å2
Displacement parametersBiso max: 43.37 Å2 / Biso mean: 15.426 Å2 / Biso min: 3.84 Å2
Baniso -1Baniso -2Baniso -3
1--1.379 Å20 Å20 Å2
2---1.438 Å20 Å2
3---2.816 Å2
Refinement stepCycle: LAST / Resolution: 1.89→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2732 0 0 252 2984
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1561.5
X-RAY DIFFRACTIONc_scbond_it2.0342
X-RAY DIFFRACTIONc_mcangle_it1.6812
X-RAY DIFFRACTIONc_scangle_it2.8632.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.89-1.920.3253460.2533716762
1.92-1.950.2519630.1958902965
1.95-1.980.2958560.1995942998
1.98-2.010.2508590.1747853912
2.01-2.040.2807390.196941980
2.04-2.080.271460.2051931977
2.08-2.120.2017420.1755912954
2.12-2.160.2717520.1811906958
2.16-2.210.2026580.1741937995
2.21-2.260.2465450.1957886931
2.26-2.320.2453440.2025943987
2.32-2.380.256520.2002924976
2.38-2.450.2799630.2127899962
2.45-2.530.303420.2265940982
2.53-2.620.1952430.1897919962
2.62-2.730.2443540.1983927981
2.73-2.850.2117550.2032938993
2.85-30.253460.2242927973
3-3.190.262440.2101952996
3.19-3.430.2486530.1991945998
3.43-3.780.2334520.1869481000
3.78-4.320.2003540.16379491003
4.32-5.430.2223480.16929861034
5.43-250.2713500.19910411091
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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