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- PDB-37bv: Crystal Structure of Thermomyces lanuginosa Lipase With Bound 1,3... -

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Basic information

Entry
Database: PDB / ID: 37bv
TitleCrystal Structure of Thermomyces lanuginosa Lipase With Bound 1,3 Diacylglycerol and Fatty Acid Acyl Intermediates: Space Group H32
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / fungus / substrates / products / acyl intermediates / interfacial activation / trimer / active form
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
DIACYL GLYCEROL / Chem-LTV / DI(HYDROXYETHYL)ETHER / 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: To Be Published
Title: Crystal Structures of Thermomyces lanuginosa Lipase With Bound 1,3 Diacylglycerol and Fatty Acid Acyl Intermediates
Authors: McPherson, A.
History
DepositionJul 12, 2026Deposition site: RCSB / Processing site: RCSB
SupersessionAug 5, 2026ID: 6O8V, 6XOK
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)37,92743
Polymers31,8361
Non-polymers6,09042
Water6,918384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-320-

CA

21A-321-

CA

31A-322-

CA

41A-441-

HOH

51A-503-

HOH

61A-648-

HOH

71A-770-

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
#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: 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 , 8 types, 425 molecules

#3: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-DGA / DIACYL GLYCEROL


Mass: 625.018 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H76O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C4H10O3
#7: 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
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: Ca
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.13 Å3/Da / Density % sol: 42.23 % / Description: long needles with two rhombic faces
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: Vapor diffusion in sitting drops. reservoirs 0.6 ml and drop size of 6 ul. reservoir 12 % Peg 3350 buffered with 0.1 M HEPES. Drop initially 3 ul of a 30 mg/ml protein stack solution plus 3 ...Details: Vapor diffusion in sitting drops. reservoirs 0.6 ml and drop size of 6 ul. reservoir 12 % Peg 3350 buffered with 0.1 M HEPES. Drop initially 3 ul of a 30 mg/ml protein stack solution plus 3 ul of reservoir. Time for crystal formation about 3 to 5 days. The protein was in the growth broth of the aspergillum expression system and was not 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: STFC Large Pixel Detector / Detector: PIXEL / Date: Dec 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→85 Å / Num. obs: 58354 / % possible obs: 87.92 % / Redundancy: 31 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.49 / Rpim(I) all: 0.49 / Rrim(I) all: 0.05 / Net I/av σ(I): 42.7 / Net I/σ(I): 8.7
Reflection shellResolution: 1.3→1.333 Å / 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: 0.29 / % possible all: 14.4

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→80.52 Å / SU ML: 0.0969 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.8082
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1566 2865 4.91 %random selection
Rwork0.1227 55489 --
obs0.1244 58354 87.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.03 Å2
Refinement stepCycle: LAST / Resolution: 1.3→80.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2008 0 384 384 2776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112500
X-RAY DIFFRACTIONf_angle_d1.60963274
X-RAY DIFFRACTIONf_chiral_restr0.094326
X-RAY DIFFRACTIONf_plane_restr0.0128397
X-RAY DIFFRACTIONf_dihedral_angle_d16.60571046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.2769140.2296459X-RAY DIFFRACTION14.42
1.33-1.350.1857680.17561178X-RAY DIFFRACTION37.91
1.35-1.380.1881150.14561748X-RAY DIFFRACTION57.01
1.38-1.410.17771030.12472327X-RAY DIFFRACTION74.11
1.41-1.440.14261300.11742686X-RAY DIFFRACTION85.57
1.44-1.470.14011930.10432831X-RAY DIFFRACTION92.31
1.47-1.510.1311590.10533015X-RAY DIFFRACTION96.07
1.51-1.550.14871430.11083079X-RAY DIFFRACTION98.53
1.55-1.590.13711320.11433189X-RAY DIFFRACTION99.91
1.59-1.640.15911650.12133095X-RAY DIFFRACTION100
1.64-1.70.17131390.13963181X-RAY DIFFRACTION100
1.7-1.770.14841570.12863142X-RAY DIFFRACTION100
1.77-1.850.15771760.11883119X-RAY DIFFRACTION99.97
1.85-1.950.16431500.11423178X-RAY DIFFRACTION100
1.95-2.070.14791480.1163176X-RAY DIFFRACTION100
2.07-2.230.14451920.11283131X-RAY DIFFRACTION100
2.23-2.460.14731540.11263196X-RAY DIFFRACTION100
2.46-2.810.13721540.1223201X-RAY DIFFRACTION100
2.81-3.540.14831780.11933222X-RAY DIFFRACTION100
3.54-80.520.18271950.13843336X-RAY DIFFRACTION99.94

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