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- PDB-4gi1: Structure of the complex of three phase partition treated lipase ... -

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Basic information

Entry
Database: PDB / ID: 4gi1
TitleStructure of the complex of three phase partition treated lipase from Thermomyces lanuginosa with 16-hydroxypalmitic acid at 2.4 A resolution
ComponentsLipase
KeywordsHYDROLASE / 16-hydroxypalmitic acid
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
16-hydroxyhexadecanoic acid / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsKumar, M. / Sinha, M. / Mukherjee, J. / Gupta, M.N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be published
Title: Structure of the complex of three phase partition treated lipase from Thermomyces lanuginosa with 16-hydroxypalmitic acid at 2.4 A resolution
Authors: Kumar, M. / Sinha, M. / Mukherjee, J. / Gupta, M.N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionAug 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4146
Polymers58,6852
Non-polymers7294
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1670 Å2
ΔGint-13 kcal/mol
Surface area20790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.837, 140.837, 80.577
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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-16Y / 16-hydroxyhexadecanoic acid


Mass: 272.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 3.93 Å3/Da / Density % sol: 68.71 %
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: May 26, 2012 / 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, L10.678
11h+k,-k,-l20.322
ReflectionResolution: 2.43→50.01 Å / Num. obs: 31439 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.101 / Net I/σ(I): 20.6
Reflection shellResolution: 2.43→2.47 Å / Mean I/σ(I) obs: 20.6 / Num. unique all: 31439 / Rsym value: 0.101 / % possible all: 96.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 2.43→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.925 / SU B: 8.365 / SU ML: 0.174 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20515 1771 5.3 %RANDOM
Rwork0.16288 ---
all0.16509 ---
obs0.16509 31439 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.671 Å2
Baniso -1Baniso -2Baniso -3
1-11.77 Å20 Å20 Å2
2--11.77 Å20 Å2
3----23.54 Å2
Refinement stepCycle: LAST / Resolution: 2.43→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 50 192 4384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224294
X-RAY DIFFRACTIONr_angle_refined_deg2.1381.9435836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2055536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32824210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.96815622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5561528
X-RAY DIFFRACTIONr_chiral_restr0.1450.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0213366
X-RAY DIFFRACTIONr_mcbond_it1.2561.52658
X-RAY DIFFRACTIONr_mcangle_it2.27224270
X-RAY DIFFRACTIONr_scbond_it3.30731636
X-RAY DIFFRACTIONr_scangle_it4.984.51566
LS refinement shellResolution: 2.43→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 117 -
Rwork0.349 2189 -
obs--95.5 %

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