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- PDB-6osz: High Resolution Structure of the Monoclinic Form of Thermomyces L... -

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Basic information

Entry
Database: PDB / ID: 6osz
TitleHigh Resolution Structure of the Monoclinic Form of Thermomyces Lanuginosa Lipase Complexed with Its Catalytic Products
ComponentsLipase
KeywordsHYDROLASE / fatty acids / diacylglycerol / acyl intermediate / LIPID BINDING PROTEIN
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 / OCTANOIC ACID (CAPRYLIC ACID) / 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: 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
DepositionMay 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)198,74140
Polymers191,0196
Non-polymers7,72234
Water31,1481729
1
A: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33019
Polymers95,5093
Non-polymers3,82116
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-55 kcal/mol
Surface area29270 Å2
MethodPISA
2
B: Lipase
C: Lipase
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,41021
Polymers95,5093
Non-polymers3,90118
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-81 kcal/mol
Surface area28520 Å2
MethodPISA
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

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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: Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#3: 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 / 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 , 5 types, 1757 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
#4: 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
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: PO4
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1729 / 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: blocks of about equal dimensions, about .30 mm edge lengths
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Sitting drop vapor diffusion at room temperature in 10 ul drops. Drops composed of equal amounts of stock protein solution, which was approximately 30 mg/ml lipase in the filtered culture ...Details: Sitting drop vapor diffusion at room temperature in 10 ul drops. Drops composed of equal amounts of stock protein solution, which was approximately 30 mg/ml lipase in the filtered culture media, and the reservoir solution. The latter was 20% PEG 3350 buffered at pH 6.5 with 0.10 M MES
PH range: 6.0 - 7.5

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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 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Mar 23, 2019
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: 19.5 % / Biso Wilson estimate: 21.03 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.036 / Rrim(I) all: 0.163 / Rsym value: 0.153 / Net I/av σ(I): 9.1 / Net I/σ(I): 9.1
Reflection shellResolution: 1.43→1.45 Å / Redundancy: 13.3 % / Rmerge(I) obs: 5.7 / Mean I/σ(I) obs: 0.4 / Num. unique obs: 15076 / CC1/2: 0.264 / Rpim(I) all: 1.66 / Rrim(I) all: 6.1 / Rsym value: 5.6 / % possible all: 98.8

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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: 1.43→76.69 Å / SU ML: 0.1965 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.3727
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1852 15362 5.01 %RANDOM
Rwork0.1486 291379 --
obs0.1504 306741 99.43 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.2 Å2
Refinement stepCycle: LAST / Resolution: 1.43→76.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12426 0 458 1729 14613
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005613401
X-RAY DIFFRACTIONf_angle_d0.923618199
X-RAY DIFFRACTIONf_chiral_restr0.07261946
X-RAY DIFFRACTIONf_plane_restr0.00962395
X-RAY DIFFRACTIONf_dihedral_angle_d20.17454950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.39014980.36179284X-RAY DIFFRACTION95.4
1.45-1.460.34474930.3259446X-RAY DIFFRACTION97.53
1.46-1.480.34665420.31369532X-RAY DIFFRACTION97.95
1.48-1.50.31954770.27899631X-RAY DIFFRACTION98.32
1.5-1.520.30725230.2639578X-RAY DIFFRACTION99.13
1.52-1.540.29274850.24899728X-RAY DIFFRACTION99.16
1.54-1.560.26285230.22899598X-RAY DIFFRACTION99.13
1.56-1.590.2785060.21859656X-RAY DIFFRACTION99.24
1.59-1.610.27564880.21679696X-RAY DIFFRACTION99.33
1.61-1.640.2335460.19299688X-RAY DIFFRACTION99.46
1.64-1.670.23695160.18459743X-RAY DIFFRACTION99.56
1.67-1.70.2245160.1679659X-RAY DIFFRACTION99.71
1.7-1.730.20785280.15139656X-RAY DIFFRACTION99.76
1.73-1.760.19615310.14379773X-RAY DIFFRACTION99.69
1.76-1.80.17985300.13159685X-RAY DIFFRACTION99.83
1.8-1.840.17914970.12589748X-RAY DIFFRACTION99.93
1.84-1.890.17315020.12319738X-RAY DIFFRACTION99.93
1.89-1.940.17735090.1349754X-RAY DIFFRACTION99.97
1.94-20.18945110.14699783X-RAY DIFFRACTION100
2-2.060.18345140.12999774X-RAY DIFFRACTION100
2.06-2.140.16815150.12499761X-RAY DIFFRACTION99.98
2.14-2.220.16734650.1169798X-RAY DIFFRACTION100
2.22-2.320.15924930.11619847X-RAY DIFFRACTION100
2.32-2.450.15725180.12389721X-RAY DIFFRACTION100
2.45-2.60.17315120.13249820X-RAY DIFFRACTION100
2.6-2.80.17995350.14069773X-RAY DIFFRACTION99.99
2.8-3.080.16835240.14329827X-RAY DIFFRACTION100
3.08-3.530.17344780.14389849X-RAY DIFFRACTION100
3.53-4.440.16184950.13189885X-RAY DIFFRACTION100
4.44-76.690.18125920.16119948X-RAY DIFFRACTION99.92

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