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- PDB-6xs3: X-ray structure of the monoclinic crystal form at 2.48 A resoluti... -

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Basic information

Entry
Database: PDB / ID: 6xs3
TitleX-ray structure of the monoclinic crystal form at 2.48 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 298 K
ComponentsLipase
KeywordsLIPID BINDING PROTEIN / substrate complex / diacylglycerol / covalent intermediate / 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
Chem-LTV / OCTANOIC ACID (CAPRYLIC ACID) / PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 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 14, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
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)198,34637
Polymers191,0196
Non-polymers7,32731
Water7,710428
1
A: Lipase
D: Lipase
F: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,08517
Polymers95,5093
Non-polymers3,57614
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-57 kcal/mol
Surface area29450 Å2
MethodPISA
2
B: Lipase
C: Lipase
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,26120
Polymers95,5093
Non-polymers3,75117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-69 kcal/mol
Surface area29160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.185, 91.366, 124.316
Angle α, β, γ (deg.)90.000, 94.700, 90.000
Int Tables number4
Space group name H-MP1211

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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: Aspergillus aculeatinus (mold) / 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.: 6
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 , 5 types, 453 molecules

#2: Chemical
ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H16O2
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: 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
#6: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 2.32 Å3/Da / Density % sol: 46.91 % / Description: cube shaped blocks
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: CXrystals were grown by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1M MES buffer. The drops were 6 ul composed of equal amounts of protein at 30 mg/ml in ...Details: CXrystals were grown by sitting drop in Cryschem plates using 0.6 ml reservoirs of 20% PEG 3350 in 0.1M MES buffer. The drops were 6 ul composed of equal amounts of protein at 30 mg/ml in water with the reservoir solution. Temperature was 298 K and crystals appeared after about two weeks
PH range: 6.0 - 7.0

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: OXFORD RUBY CCD / Detector: CCD / Date: Jun 20, 2017
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.48→75 Å / Num. obs: 81074 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 26 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.292 / Rpim(I) all: 0.102 / Rrim(I) all: 0.327 / Rsym value: 0.287 / Net I/σ(I): 7.1
Reflection shellResolution: 2.48→2.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4362 / CC1/2: 0.18 / Rpim(I) all: 0.62 / Rrim(I) all: 1.3 / Rsym value: 1.01 / % possible all: 96.2

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 2.48→51.27 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.19 / Stereochemistry target values: ML
Details: Structure was refined to convergence with REFMAC5 in CCP4, then five runs through PHENIX REFINE using isotropic B values and no TLS.
RfactorNum. reflection% reflection
Rfree0.2134 3025 4.91 %
Rwork0.1783 58636 -
obs0.1801 61661 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164 Å2 / Biso mean: 36.1154 Å2 / Biso min: 9.62 Å2
Refinement stepCycle: final / Resolution: 2.48→51.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12425 0 508 430 13363
Biso mean--72.84 32.57 -
Num. residues----1614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.48-2.520.3481310.3142533266494
2.52-2.560.27621500.29582564271498
2.56-2.60.3291210.27912683280499
2.6-2.650.30721350.26882627276299
2.65-2.70.28831470.25942659280699
2.7-2.760.28871420.246726482790100
2.76-2.820.2611470.235326472794100
2.82-2.880.24451370.226326522789100
2.88-2.960.26061430.208626722815100
2.96-3.040.24111530.204426502803100
3.04-3.130.23041340.19426772811100
3.13-3.230.23231410.188526532794100
3.23-3.340.23651370.177626752812100
3.34-3.480.21861440.175426582802100
3.48-3.630.1731240.153327042828100
3.63-3.820.17221250.142526852810100
3.83-4.060.19611280.13926852813100
4.06-4.380.15981330.129626822815100
4.38-4.820.16851450.11527112856100
4.82-5.510.15291260.129327032829100
5.51-6.940.17561310.151227172848100
6.95-51.270.16711510.157627512902100

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