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- PDB-4ea6: Crystal structure of Fungal lipase from Thermomyces(Humicola) lan... -

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Basic information

Entry
Database: PDB / ID: 4ea6
TitleCrystal structure of Fungal lipase from Thermomyces(Humicola) lanuginosa at 2.30 Angstrom resolution.
ComponentsLipase
KeywordsHYDROLASE
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, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKumar, M. / Mukherjee, J. / Gupta, M.N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of Fungal lipase from Thermomyces(Humicola) lanuginosa at 2.30 Angstrom resolution.
Authors: Kumar, M. / Mukherjee, J. / Gupta, M.N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase


Theoretical massNumber of molelcules
Total (without water)58,6852
Polymers58,6852
Non-polymers00
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1180 Å2
ΔGint-13 kcal/mol
Surface area20770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.180, 140.180, 80.582
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Lipase / Triacylglycerol lipase


Mass: 29342.484 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O
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: 3.89 Å3/Da / Density % sol: 68.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, O.1M Nacl, 1.6M Ammonium sulphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 9, 2011 / Details: mirror
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.527
11K, H, -L20.473
ReflectionResolution: 2.3→50.01 Å / Num. all: 37931 / Num. obs: 37931 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 37.5 Å2 / Rsym value: 0.083 / Net I/σ(I): 15.5
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.346 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DT3

1dt3


Resolution: 2.3→50.01 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.356 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.049 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22989 2012 5 %RANDOM
Rwork0.21317 ---
all0.21403 37931 --
obs0.21403 37931 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.179 Å2
Baniso -1Baniso -2Baniso -3
1-20.29 Å20 Å20 Å2
2--20.29 Å20 Å2
3----40.58 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 0 243 4385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.024248
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9345790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.80224210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.73815622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6651528
X-RAY DIFFRACTIONr_chiral_restr0.060.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213358
LS refinement shellResolution: 2.301→2.34 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 113 -
Rwork0.226 2741 -
obs--98.21 %

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