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- PDB-6jd9: Proteus mirabilis lipase mutant - I118V/E130G -

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Basic information

Entry
Database: PDB / ID: 6jd9
TitleProteus mirabilis lipase mutant - I118V/E130G
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / Lipase / Proteus mirabilis lipase
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / metal ion binding
Similarity search - Function
alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha/beta hydrolase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsHeater, B.S. / Chan, W.S. / Chan, M.K.
Funding support Hong Kong, 1items
OrganizationGrant numberCountry
14323216 Hong Kong
CitationJournal: Biotechnol Biofuels / Year: 2019
Title: Directed evolution of a genetically encoded immobilized lipase for the efficient production of biodiesel from waste cooking oil.
Authors: Heater, B.S. / Chan, W.S. / Lee, M.M. / Chan, M.K.
History
DepositionJan 31, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7394
Polymers31,4621
Non-polymers2763
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area810 Å2
ΔGint-30 kcal/mol
Surface area12230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.310, 65.310, 63.591
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Alpha/beta hydrolase / Lipase


Mass: 31462.359 Da / Num. of mol.: 1 / Mutation: I118V, E130G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: lip, AM402_13560, NCTC10975_00950 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1Z1SX23, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 70% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 16, 2018
RadiationMonochromator: LN2-Cooled, Fixed-Exit Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→63.59 Å / Num. obs: 41629 / % possible obs: 100 % / Redundancy: 5.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.039 / Rrim(I) all: 0.091 / Net I/σ(I): 16.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.58-1.615.50.1320590.9820.0610.144100
8.65-63.594.70.092520.8910.0520.10597.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASERphasing
REFMAC5.8.0135refinement
PDB_EXTRACT3.24data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→19.85 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.025 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.064 / ESU R Free: 0.065
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1626 2089 5 %RANDOM
Rwork0.1388 ---
obs0.14 39488 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 75.66 Å2 / Biso mean: 15.038 Å2 / Biso min: 5.15 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: final / Resolution: 1.58→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 17 215 2452
Biso mean--21.24 25.47 -
Num. residues----286
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0192282
X-RAY DIFFRACTIONr_bond_other_d0.0020.022160
X-RAY DIFFRACTIONr_angle_refined_deg2.3531.953096
X-RAY DIFFRACTIONr_angle_other_deg1.21234947
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1785285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.24124.679109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26915366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1351510
X-RAY DIFFRACTIONr_chiral_restr0.1570.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022644
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02548
LS refinement shellResolution: 1.58→1.621 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.192 160 -
Rwork0.144 2913 -
all-3073 -
obs--100 %

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