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- PDB-37cb: Crystal Structure of Thermomyces lanuginosa Lipase with acyl inte... -

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Basic information

Entry
Database: PDB / ID: 37cb
TitleCrystal Structure of Thermomyces lanuginosa Lipase with acyl intermediate: space group I222
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / acyl intermediate / fungal / hydrolase / substrate / crystallization
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
DI(HYDROXYETHYL)ETHER / PALMITIC ACID / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Thermomyces lanuginosa Lipase with acyl intermediate: space group I222
Authors: McPherson, A.
History
DepositionJul 13, 2026Deposition site: RCSB / Processing site: RCSB
SupersessionAug 5, 2026ID: 6OR3
Revision 1.0Aug 5, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,38122
Polymers31,8361
Non-polymers2,54421
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.865, 85.268, 86.741
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-615-

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: Aspergillus (fungus) / 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.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
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 , 7 types, 235 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: 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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Details

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: 2.03 Å3/Da / Density % sol: 39.38 % / Description: rectangular blocks
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystallized by sitting drop vapor diffusion with reservoirs of 0.6 ml and drop volumes of 6 ul. Reservoirs were 20% PEG 3350 with 0.1 M HEPES at pH 6.0. Drops were equal amounts of the ...Details: Crystallized by sitting drop vapor diffusion with reservoirs of 0.6 ml and drop volumes of 6 ul. Reservoirs were 20% PEG 3350 with 0.1 M HEPES at pH 6.0. Drops were equal amounts of the reservoir and a 30 mg/ml stock protein solution. The solution was the raw growth broth for the Aspergillus expression system and the protein was not otherwise purified,
PH range: 4.5 - 6.0

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Data collection

DiffractionMean temperature: 173 K / Crystal support: Mitigen tips / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→61 Å / Num. obs: 46198 / % possible obs: 99.9 % / Redundancy: 62.8 % / Biso Wilson estimate: 23.17 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.334 / Rpim(I) all: 0.39 / Rrim(I) all: 0.337 / Rsym value: 0.336 / Net I/σ(I): 10.4
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 38.7 % / Rmerge(I) obs: 3.6 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2213 / CC1/2: 0.29 / Rpim(I) all: 0.58 / Rrim(I) all: 3.7 / Rsym value: 3.7 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→60.81 Å / SU ML: 0.2337 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.6715
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2352 2287 4.96 %
Rwork0.1605 43857 -
obs0.1641 46144 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.04 Å2
Refinement stepCycle: LAST / Resolution: 1.45→60.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 158 215 2444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01042307
X-RAY DIFFRACTIONf_angle_d1.25293095
X-RAY DIFFRACTIONf_chiral_restr0.0834327
X-RAY DIFFRACTIONf_plane_restr0.0107400
X-RAY DIFFRACTIONf_dihedral_angle_d15.4109888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.480.43241640.39442655X-RAY DIFFRACTION98.91
1.48-1.520.41191510.34952704X-RAY DIFFRACTION99.86
1.52-1.550.34341350.32852742X-RAY DIFFRACTION99.86
1.55-1.60.32421350.28232703X-RAY DIFFRACTION99.89
1.6-1.640.30281410.26162711X-RAY DIFFRACTION99.89
1.64-1.70.31461710.24932668X-RAY DIFFRACTION99.93
1.7-1.760.3281440.24822729X-RAY DIFFRACTION99.97
1.76-1.830.31051410.22342707X-RAY DIFFRACTION99.96
1.83-1.910.23961130.1962770X-RAY DIFFRACTION99.9
1.91-2.010.21631390.17732736X-RAY DIFFRACTION100
2.01-2.140.28371450.16462740X-RAY DIFFRACTION99.86
2.14-2.30.20171520.15422719X-RAY DIFFRACTION99.97
2.3-2.530.23321300.1472782X-RAY DIFFRACTION99.93
2.53-2.90.24161490.1412771X-RAY DIFFRACTION99.86
2.9-3.650.21171470.1242787X-RAY DIFFRACTION100
3.65-60.810.19771300.13282933X-RAY DIFFRACTION99.97

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