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- PDB-6xok: X-ray structure of the rhombohedral form of the lipase from Therm... -

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Basic information

Entry
Database: PDB / ID: 6xok
TitleX-ray structure of the rhombohedral form of the lipase from Thermomyces lanuginosa at 1.3 A resolution
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / diacylglyceride / interfacial activation / oligomer / substrate complex
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 / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMcPherson, A.
CitationJournal: Current Enzyme Inhibition / Year: 2020
Title: The crystal Structures of Thermomyces (Humicola) lanuginosa lipase in complex with enzymatic reactants
Authors: McPherson, A. / Larson, S.B. / Kalasky, A.
History
DepositionJul 7, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)33,54510
Polymers31,8361
Non-polymers1,7089
Water7,692427
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lipase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)201,27060
Polymers191,0196
Non-polymers10,25154
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area22650 Å2
ΔGint-214 kcal/mol
Surface area56500 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"
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-244-

THR

21A-307-

PO4

31A-307-

PO4

41A-686-

HOH

51A-801-

HOH

61A-816-

HOH

71A-819-

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 flavus (mold) / 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
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, 435 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.: 6 / 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.: 427 / 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: Crystals were grown by vapor diffusion at room temperature in 24 well Cryschem sitting drop plates (Hampton Research, Aliso Viejo, CA) with 600 microleters reservoirs of 25% PEG 3350 in 0.10 ...Details: Crystals were grown by vapor diffusion at room temperature in 24 well Cryschem sitting drop plates (Hampton Research, Aliso Viejo, CA) with 600 microleters reservoirs of 25% PEG 3350 in 0.10 M MES buffer at pH 6.5. The protein droplets were of 8ul volume and consisted of equal parts of a 20 to 30 mg/ml protein stock solution and the reservoir solution. Crystals usually appeared and grew to full size within one to two weeks. Rhombohedral crystals were thin needles of indeterminate cross-section
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 173 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.03 Å
DetectorType: DECTRIS PILATUS3 X CdTe 1M / Detector: PIXEL / Date: Feb 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.3→80 Å / Num. obs: 58358 / % possible obs: 88 % / Redundancy: 31 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.008 / Rrim(I) all: 0.05 / Rsym value: 0.049 / 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: 0.36 / % possible all: 14.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 1.3→80 Å / SU ML: 0.0786 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 12.3452
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Details: Structure was thoroughly refined using REFMAC5 from CCP4 but then refined further using REFINE from PHENIX. Some improvements, such as addition of aa 241-244 at the cleavage site were made ...Details: Structure was thoroughly refined using REFMAC5 from CCP4 but then refined further using REFINE from PHENIX. Some improvements, such as addition of aa 241-244 at the cleavage site were made in REFINE. The restraints for the diglyceride substrate were made in the GRADE server. Waters were added by hand.
RfactorNum. reflection% reflection
Rfree0.1343 2865 4.91 %
Rwork0.1041 55488 -
obs0.1056 58353 87.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.44 Å2
Refinement stepCycle: LAST / Resolution: 1.3→80 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2015 0 108 427 2550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00792340
X-RAY DIFFRACTIONf_angle_d1.24433189
X-RAY DIFFRACTIONf_chiral_restr0.0991342
X-RAY DIFFRACTIONf_plane_restr0.0072410
X-RAY DIFFRACTIONf_dihedral_angle_d20.1882
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.330.1926140.1575459X-RAY DIFFRACTION14.42
1.33-1.350.1646680.11691178X-RAY DIFFRACTION37.91
1.35-1.380.1411150.10061748X-RAY DIFFRACTION57.01
1.38-1.410.15341030.08672327X-RAY DIFFRACTION74.11
1.41-1.440.13711300.082686X-RAY DIFFRACTION85.57
1.44-1.470.11931930.07562831X-RAY DIFFRACTION92.31
1.47-1.510.11581590.07153015X-RAY DIFFRACTION96.07
1.51-1.550.12521430.07613079X-RAY DIFFRACTION98.53
1.55-1.590.1141320.07563189X-RAY DIFFRACTION99.91
1.59-1.640.12121650.07993095X-RAY DIFFRACTION100
1.64-1.70.12971390.08113181X-RAY DIFFRACTION100
1.7-1.770.11821570.08853142X-RAY DIFFRACTION100
1.77-1.850.12991760.08633119X-RAY DIFFRACTION99.97
1.85-1.950.12911500.08813178X-RAY DIFFRACTION100
1.95-2.070.11481480.08743176X-RAY DIFFRACTION100
2.07-2.230.12951920.08783131X-RAY DIFFRACTION100
2.23-2.460.11741540.09483196X-RAY DIFFRACTION100
2.46-2.810.12851540.11273201X-RAY DIFFRACTION100
2.81-3.540.14171780.11363222X-RAY DIFFRACTION100
3.54-80.520.15561950.14173335X-RAY DIFFRACTION99.92

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