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- PDB-6xrv: X-ray structure of the monoclinic crystal form at 1.43 A resoluti... -

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Basic information

Entry
Database: PDB / ID: 6xrv
TitleX-ray structure of the monoclinic crystal form at 1.43 A resolution of lipase from Thermomyces (Humicola) lanuginosa at 173 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 13, 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)198,64639
Polymers191,0196
Non-polymers7,62733
Water29,1481618
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 area7020 Å2
ΔGint-59 kcal/mol
Surface area29080 Å2
MethodPISA
2
B: Lipase
C: Lipase
E: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,31520
Polymers95,5093
Non-polymers3,80617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6880 Å2
ΔGint-73 kcal/mol
Surface area28810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.929, 89.937, 123.422
Angle α, β, γ (deg.)90.000, 94.490, 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
#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: 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, 1645 molecules

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


Mass: 144.211 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C8H16O2
#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.: 9 / Source method: obtained synthetically / 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.: 1618 / 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: cube like blocks
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals grown by sitting drop with 0.6 ul reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops of 8 ul composed of equal amounts of the protein at 30.0 mg/ml in water with the ...Details: Crystals grown by sitting drop with 0.6 ul reservoirs of 20% PEG 3350 in 0.1 M MES buffer at pH 6.5. Drops of 8 ul composed of equal amounts of the protein at 30.0 mg/ml in water with the reservoir solution. Room temperature throughout, crystals grew in about a month
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 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 22, 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: 19.2 % / Biso Wilson estimate: 22 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.036 / Rrim(I) all: 0.163 / Rsym value: 0.156 / Net I/σ(I): 9.1
Reflection shellResolution: 1.43→1.45 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 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TIB

1tib


Resolution: 1.43→77 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.66 / Stereochemistry target values: ML
Details: Refined to convergence in REFMAC then subjected to further rebuilding in COOT and an additional 15 runs in REFINE from PHENIX. Anisotropic B values, no TLS.
RfactorNum. reflection% reflection
Rfree0.1871 15362 5.01 %
Rwork0.1495 291380 -
obs0.1514 306742 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.3 Å2 / Biso mean: 29.7343 Å2 / Biso min: 8.46 Å2
Refinement stepCycle: final / Resolution: 1.43→77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12425 0 531 1628 14584
Biso mean--54.53 38.88 -
Num. residues----1614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.43-1.450.38544980.35619284978295
1.45-1.460.34124930.32339446993998
1.46-1.480.34335420.311795321007498
1.48-1.50.3154770.279196311010898
1.5-1.520.31235230.262595781010199
1.52-1.540.29364850.247397281021399
1.54-1.560.26355230.223695981012199
1.56-1.590.26955060.206596561016299
1.59-1.610.25084880.193596961018499
1.61-1.640.21925460.172296881023499
1.64-1.670.22635160.1687974310259100
1.67-1.70.21695160.1576965910175100
1.7-1.730.20185280.1454965610184100
1.73-1.760.19555310.1423977310304100
1.76-1.80.18275300.1333968510215100
1.8-1.840.18124970.1272974810245100
1.84-1.890.17795020.1242973810240100
1.89-1.940.17245090.1287975410263100
1.94-20.18415110.1354978310294100
2-2.060.17685140.129977410288100
2.06-2.140.17355150.128976110276100
2.14-2.220.16964650.1201979810263100
2.22-2.320.16434930.1202984710340100
2.32-2.450.15845180.1259972110239100
2.45-2.60.17225120.1322982010332100
2.6-2.80.1865350.1425977310308100
2.8-3.080.16885240.147982710351100
3.08-3.530.17814780.1477984910327100
3.53-4.440.17044950.1361988510380100
4.44-76.690.18485920.1647994910541100

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