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- PDB-4zgb: Structure of untreated lipase from Thermomyces lanuginosa at 2.3 ... -

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Basic information

Entry
Database: PDB / ID: 4zgb
TitleStructure of untreated lipase from Thermomyces lanuginosa at 2.3 A 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. / Sinha, M. / Mukherjee, J. / Gupta, M.N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Sustain Chem Process / Year: 2015
Title: Enhancement of stability of a lipase by subjecting to three phase partitioning (TPP): structures of native and TPP-treated lipase from Thermomyces lanuginosa
Authors: Kumar, M. / Mukherjee, J. / Sinha, M. / Kaur, P. / Sharma, S. / Gupta, M.N. / Singh, T.P.
History
DepositionApr 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 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
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1130 Å2
ΔGint-12 kcal/mol
Surface area20800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.131, 140.131, 80.504
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.: 240 / 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: 3.8 Å3/Da / Density % sol: 67.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, O.1M Nacl, 1.6M Ammonium sulphate / PH range: 7.5

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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 20, 2011
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, L10.488
11K, H, -L20.512
ReflectionResolution: 2.3→50 Å / Num. obs: 37653 / % possible obs: 98.8 % / Redundancy: 4.3 % / Rsym value: 0.069 / Net I/σ(I): 4
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 0.26 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 2.3→48.46 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.395 / SU ML: 0.109 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20644 1925 4.9 %RANDOM
Rwork0.18086 ---
obs0.18207 37653 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.58 Å2
Baniso -1Baniso -2Baniso -3
1-17.9 Å2-0 Å20 Å2
2--17.9 Å20 Å2
3----35.81 Å2
Refinement stepCycle: 1 / Resolution: 2.3→48.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 0 240 4382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0194248
X-RAY DIFFRACTIONr_bond_other_d0.0030.023850
X-RAY DIFFRACTIONr_angle_refined_deg2.231.9315786
X-RAY DIFFRACTIONr_angle_other_deg1.26438826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8715536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.10224210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49615622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0131528
X-RAY DIFFRACTIONr_chiral_restr0.1340.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021050
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.414.1642150
X-RAY DIFFRACTIONr_mcbond_other4.4114.1642149
X-RAY DIFFRACTIONr_mcangle_it5.8776.2342684
X-RAY DIFFRACTIONr_mcangle_other5.8756.2342685
X-RAY DIFFRACTIONr_scbond_it4.3414.222098
X-RAY DIFFRACTIONr_scbond_other4.3414.222098
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6466.2643102
X-RAY DIFFRACTIONr_long_range_B_refined8.37733.7765192
X-RAY DIFFRACTIONr_long_range_B_other8.333.7355136
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 97 -
Rwork0.236 2579 -
obs--91.24 %

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