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- PDB-6o9f: The structure of Thermomyces Lanuginosa lipase in complex with 1,... -

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Basic information

Entry
Database: PDB / ID: 6o9f
TitleThe structure of Thermomyces Lanuginosa lipase in complex with 1,3 diacylglycerol in a monoclinic crystal form
ComponentsLipase
KeywordsHYDROLASE / lipids / triglycerides / catalytic triad / monolayer / acyl intermediate / trimer / NCS / LIPID BINDING PROTEIN
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
Mono-/di-acylglycerol lipase, N-terminal / Lipase 3 N-terminal region / : / Fungal lipase-like domain / Lipase (class 3) / Lipases, serine active site. / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Chem-LTV / OCTANOIC ACID (CAPRYLIC ACID) / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Curr Enzym Inhib / Year: 2020
Title: The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants
Authors: McPherson , A. / Larson , B.S. / Kalasky , A.
History
DepositionMar 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
B: Lipase
C: Lipase
E: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,34637
Polymers191,0196
Non-polymers7,32731
Water7,710428
1
A: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,08517
Polymers95,5093
Non-polymers3,57614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-56 kcal/mol
Surface area29460 Å2
MethodPISA
2
B: Lipase
C: Lipase
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,26120
Polymers95,5093
Non-polymers3,75117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-70 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.185, 91.366, 124.316
Angle α, β, γ (deg.)90.000, 94.705, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

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Protein / Sugars , 2 types, 12 molecules ABCEDF

#1: Protein
Lipase / Triacylglycerol lipase


Mass: 31836.459 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Gene: LIP / Production host: Thermoactinomyces vulgaris (bacteria) / References: UniProt: O59952, triacylglycerol lipase
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 453 molecules

#2: Chemical
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H16O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: Ca
#5: Chemical
ChemComp-LTV / 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate


Mass: 723.204 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C46H90O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.91 %
Description: Thick equidimensional blocks 0.25 to 0.50 mm edge lengths
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein source was a filtered fungal culture medium at about 50 mg/ml. This was combined in 8 ul drops with equal amounts of 25% PEG 3350 buffered at pH 6.5 with 0.10 M MES and crystallized ...Details: Protein source was a filtered fungal culture medium at about 50 mg/ml. This was combined in 8 ul drops with equal amounts of 25% PEG 3350 buffered at pH 6.5 with 0.10 M MES and crystallized at room temperature by sitting drops in Cryschem plates
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: May 15, 2016
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.48→80 Å / Num. obs: 81074 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 27.29 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.102 / Rrim(I) all: 0.327 / Rsym value: 0.245 / Net I/av σ(I): 7.1 / Net I/σ(I): 7.1
Reflection shellResolution: 2.48→2.52 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4362 / CC1/2: 0.18 / Rpim(I) all: 0.623 / Rrim(I) all: 1.3 / Rsym value: 0.85 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.48→51.27 Å / SU ML: 0.3209 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.021
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 3025 4.91 %RANDOM
Rwork0.1749 58636 --
obs0.1768 61661 99.54 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.59 Å2
Refinement stepCycle: LAST / Resolution: 2.48→51.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12425 0 431 428 13284
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002513396
X-RAY DIFFRACTIONf_angle_d0.520818197
X-RAY DIFFRACTIONf_chiral_restr0.04181945
X-RAY DIFFRACTIONf_plane_restr0.00392398
X-RAY DIFFRACTIONf_dihedral_angle_d14.44914951
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.520.34711310.30722533X-RAY DIFFRACTION94.23
2.52-2.560.27941500.28932564X-RAY DIFFRACTION98.23
2.56-2.60.33531210.27092683X-RAY DIFFRACTION99.43
2.6-2.650.30191350.25862627X-RAY DIFFRACTION99.28
2.65-2.70.28761470.25062659X-RAY DIFFRACTION99.33
2.7-2.760.28921420.24042648X-RAY DIFFRACTION100
2.76-2.820.25371470.23212647X-RAY DIFFRACTION100
2.82-2.880.25041370.22032652X-RAY DIFFRACTION99.96
2.88-2.960.2551430.20272672X-RAY DIFFRACTION100
2.96-3.040.24291530.19632650X-RAY DIFFRACTION99.93
3.04-3.130.2231340.18852677X-RAY DIFFRACTION100
3.13-3.230.23331410.1822653X-RAY DIFFRACTION99.93
3.23-3.340.2361370.17412675X-RAY DIFFRACTION100
3.34-3.480.22021440.17362658X-RAY DIFFRACTION99.96
3.48-3.630.18011240.15122704X-RAY DIFFRACTION100
3.63-3.820.17511250.13972685X-RAY DIFFRACTION100
3.83-4.060.1991280.13662685X-RAY DIFFRACTION100
4.06-4.380.15631330.12692682X-RAY DIFFRACTION100
4.38-4.820.17121450.11372711X-RAY DIFFRACTION100
4.82-5.510.16161260.12872703X-RAY DIFFRACTION100
5.51-6.940.17951310.15052717X-RAY DIFFRACTION99.96
6.95-51.270.16621510.15872751X-RAY DIFFRACTION99.59

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