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- PDB-6o8v: The structure of lipase from Thermomyces Lanuginosa in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6o8v
TitleThe structure of lipase from Thermomyces Lanuginosa in complex with 1,3 diacylglycerol: Rhombohedral crystal form
ComponentsLipase
KeywordsHYDROLASE / trimer / esterase / lipids / lipase / substrate complex / catalysis / acyl intermediate / LIPID BINDING PROTEIN
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride 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 / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4509
Polymers31,8361
Non-polymers1,6138
Water7,296405
1
A: Lipase
hetero molecules

A: Lipase
hetero molecules

A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,35027
Polymers95,5093
Non-polymers4,84024
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area7810 Å2
ΔGint-79 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.373, 76.373, 241.551
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Components on special symmetry positions
IDModelComponents
11A-691-

HOH

21A-731-

HOH

31A-780-

HOH

41A-793-

HOH

51A-796-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Lipase / Triacylglycerol lipase


Mass: 31836.459 Da / Num. of mol.: 1
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
#2: 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.: 1
Source method: isolated from a genetically manipulated source
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 , 4 types, 412 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-LTV / 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate


Mass: 723.204 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H90O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.23 % / Description: thin needles of indeterminate cross section
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: From a filtered, crude nutrient broth containing 30 - 50 mg/ml lipase plus 25% PEG 3350 plus 0.10 M MES buffer at room temperature
PH range: 6.0 - 7.5

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Data collection

DiffractionMean temperature: 173 K / Ambient temp details: flash frozen in cryostream / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.3→100 Å / Num. obs: 58358 / % possible obs: 88 % / Redundancy: 31 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.01 / Rrim(I) all: 0.05 / Rsym value: 0.046 / Net I/av σ(I): 42.7 / Net I/σ(I): 42.7
Reflection shellResolution: 1.3→1.33 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 463 / CC1/2: 0.81 / Rpim(I) all: 0.205 / Rrim(I) all: 0.461 / Rsym value: 0.34 / % possible all: 14.4

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Processing

Software
NameVersionClassification
PHENIX1.19rc7_4070refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tib

1tib


Resolution: 1.3→80.52 Å / SU ML: 0.0934 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 13.2256
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1413 2865 4.91 %RANDOM
Rwork0.1094 55487 --
obs0.111 58352 87.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.61 Å2
Refinement stepCycle: LAST / Resolution: 1.3→80.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2012 0 103 405 2520
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00972230
X-RAY DIFFRACTIONf_angle_d1.15453035
X-RAY DIFFRACTIONf_chiral_restr0.0927326
X-RAY DIFFRACTIONf_plane_restr0.0184390
X-RAY DIFFRACTIONf_dihedral_angle_d11.3834826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.348140.2164459X-RAY DIFFRACTION14.42
1.33-1.350.183680.15461178X-RAY DIFFRACTION37.91
1.35-1.380.16491150.12011748X-RAY DIFFRACTION57.01
1.38-1.410.1721030.09492327X-RAY DIFFRACTION74.11
1.41-1.440.14551300.08222686X-RAY DIFFRACTION85.57
1.44-1.470.12431930.0772831X-RAY DIFFRACTION92.31
1.47-1.510.1321590.07863015X-RAY DIFFRACTION96.07
1.51-1.550.12721430.08613079X-RAY DIFFRACTION98.53
1.55-1.590.13131320.08773189X-RAY DIFFRACTION99.91
1.59-1.640.14771650.09733095X-RAY DIFFRACTION100
1.64-1.70.18041390.11823181X-RAY DIFFRACTION100
1.7-1.770.14471570.10043142X-RAY DIFFRACTION100
1.77-1.850.14131760.08953119X-RAY DIFFRACTION99.97
1.85-1.950.13111500.08973178X-RAY DIFFRACTION100
1.95-2.070.12941480.09483176X-RAY DIFFRACTION100
2.07-2.230.13711920.08973131X-RAY DIFFRACTION100
2.23-2.460.11361540.0943196X-RAY DIFFRACTION100
2.46-2.810.13011540.11333201X-RAY DIFFRACTION100
2.81-3.540.14381780.11713222X-RAY DIFFRACTION100
3.54-80.520.15551950.14423334X-RAY DIFFRACTION99.89

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