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

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Basic information

Entry
Database: PDB / ID: 37ds
TitleCrystal Structure of Thermomyces lanuginosa Lipase With Bound 1,3 diacylglycrol and Fatty Acid Acyl intermediates: Monoclinic Crystals
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / catalytic intermediates / trimer / substrates / products / lid opening / interfacial activation
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
ACETATE ION / Chem-LTV / OCTANOIC ACID (CAPRYLIC ACID) / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsMcPherson, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal Structure of Thermomyces lanuginosa Lipase With Bound 1,3 diacylglycrol and Fatty Acid Acyl intermediates: Monoclinic Crystals
Authors: McPherson, A.
History
DepositionJul 15, 2026Deposition site: RCSB / Processing site: RCSB
SupersessionAug 5, 2026ID: 6XRV
Revision 1.0Aug 5, 2026Provider: 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
B: Lipase
C: Lipase
E: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,02699
Polymers191,0196
Non-polymers14,00793
Water42,4972359
1
A: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,32319
Polymers31,8361
Non-polymers2,48718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,50416
Polymers31,8361
Non-polymers1,66815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,82821
Polymers31,8361
Non-polymers2,99220
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,85517
Polymers31,8361
Non-polymers3,01916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
D: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,15017
Polymers31,8361
Non-polymers2,31416
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3649
Polymers31,8361
Non-polymers1,5288
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.929, 89.937, 123.422
Angle α, β, γ (deg.)90.000, 94.488, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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: Aspergillaceae sp. (fungus) / References: UniProt: O59952, triacylglycerol lipase
#8: 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
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 , 10 types, 2446 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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical...
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 40 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#9: Chemical
ChemComp-LTV / 2-hydroxy-3-(octadecanoyloxy)propyl pentacosanoate


Mass: 723.204 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C46H90O5 / Feature type: SUBJECT OF INVESTIGATION
#10: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#11: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2359 / 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: 2.23 Å3/Da / Density % sol: 44.8 % / Description: monoclinic prisms
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Crystallized by sitting drop vapor diffusion with 0.6 ml reservoirs and drop volumes 6 ul. Drops consisted of equal volumes of the reservoir and the protein stock solution. The reservoirs ...Details: Crystallized by sitting drop vapor diffusion with 0.6 ml reservoirs and drop volumes 6 ul. Drops consisted of equal volumes of the reservoir and the protein stock solution. The reservoirs were 20% w/v PEG 3350 with 0.1 M HEPES buffer. The protein was in the growth broth of the aspergillum expression system and was not further purified. The stock protein concentration was 30 mg/ml
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 19, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.43→77 Å / Num. obs: 307462 / % possible obs: 99.7 % / Redundancy: 19.2 % / Biso Wilson estimate: 21.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.36 / Rrim(I) all: 0.163 / Rsym value: 0.146 / Net I/σ(I): 9.1
Reflection shellResolution: 1.43→1.47 Å / Redundancy: 13.3 % / Rmerge(I) obs: 5.69 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 15076 / CC1/2: 0.26 / Rpim(I) all: 1.66 / Rrim(I) all: 6.1 / Rsym value: 4.85 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→76.69 Å / SU ML: 0.1982 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.2446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1811 15362 5.01 %
Rwork0.1301 291378 -
obs0.1326 306740 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.28 Å2
Refinement stepCycle: LAST / Resolution: 1.43→76.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12423 0 833 2359 15615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007713784
X-RAY DIFFRACTIONf_angle_d1.012318576
X-RAY DIFFRACTIONf_chiral_restr0.07841958
X-RAY DIFFRACTIONf_plane_restr0.00882411
X-RAY DIFFRACTIONf_dihedral_angle_d16.83195271
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.38864980.35449284X-RAY DIFFRACTION95.4
1.45-1.460.34384930.31759446X-RAY DIFFRACTION97.53
1.46-1.480.34035420.30319532X-RAY DIFFRACTION97.95
1.48-1.50.32164770.27279631X-RAY DIFFRACTION98.32
1.5-1.520.315230.25679578X-RAY DIFFRACTION99.13
1.52-1.540.29914850.24219728X-RAY DIFFRACTION99.16
1.54-1.560.26715230.22049598X-RAY DIFFRACTION99.13
1.56-1.590.2725060.2119656X-RAY DIFFRACTION99.24
1.59-1.610.27794880.21269696X-RAY DIFFRACTION99.33
1.61-1.640.24125460.19199688X-RAY DIFFRACTION99.46
1.64-1.670.23435160.17499743X-RAY DIFFRACTION99.56
1.67-1.70.2265160.16059659X-RAY DIFFRACTION99.71
1.7-1.730.20785280.14649656X-RAY DIFFRACTION99.76
1.73-1.760.20575310.14169773X-RAY DIFFRACTION99.69
1.76-1.80.17485300.12449685X-RAY DIFFRACTION99.83
1.8-1.840.18364970.11759748X-RAY DIFFRACTION99.93
1.84-1.890.17235020.1189738X-RAY DIFFRACTION99.93
1.89-1.940.18465090.13199754X-RAY DIFFRACTION99.97
1.94-20.19935110.14589783X-RAY DIFFRACTION100
2-2.060.18225140.12629774X-RAY DIFFRACTION100
2.06-2.140.17035150.11869761X-RAY DIFFRACTION99.98
2.14-2.220.16584650.1099798X-RAY DIFFRACTION100
2.22-2.320.15884930.1059847X-RAY DIFFRACTION100
2.32-2.450.1555180.10739721X-RAY DIFFRACTION100
2.45-2.60.15935120.11289820X-RAY DIFFRACTION100
2.6-2.80.16615350.11529773X-RAY DIFFRACTION99.99
2.8-3.080.16285240.11689827X-RAY DIFFRACTION100
3.08-3.530.1584780.11289849X-RAY DIFFRACTION100
3.53-4.440.16334950.10259885X-RAY DIFFRACTION100
4.44-76.690.17235920.13469947X-RAY DIFFRACTION99.91

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