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- PDB-4kjx: Crystal Structure of the complex of three phase partition treated... -

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Basic information

Entry
Database: PDB / ID: 4kjx
TitleCrystal Structure of the complex of three phase partition treated lipase from Thermomyces lanuginosa with Lauric acid and P-nitrobenzaldehyde (PNB) at 2.1 resolution
ComponentsLipase
KeywordsHYDROLASE
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride 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
ACETATE ION / LAURIC ACID / 4-nitrobenzaldehyde / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 the complex of three phase partition treated lipase from Thermomyces lanuginosa with Lauric acid and P-nitrobenzaldehyde (PNB) at 2.1 resolution
Authors: Kumar, M. / Mukherjee, J. / Gupta, M.N. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 4, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,35315
Polymers58,6852
Non-polymers1,66813
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint1 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.997, 139.997, 80.492
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Lipase / / Triacylglycerol lipase


Mass: 29342.484 Da / Num. of mol.: 2 / Fragment: UNP residues 23-291 / Source method: isolated from a natural source / Source: (natural) Thermomyces lanuginosus (fungus) / References: UniProt: O59952, triacylglycerol lipase
#2: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 6 types, 280 molecules

#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-DAO / LAURIC ACID / Lauric acid


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-XXH / 4-nitrobenzaldehyde / Nitrobenzaldehyde


Mass: 151.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5NO3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.3 %
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 18, 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
ReflectionResolution: 2.1→50 Å / Num. all: 98715 / Num. obs: 48911 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 40.5 Å2 / Rsym value: 0.086 / Net I/σ(I): 35.3
Reflection shellResolution: 2.1→2.14 Å / Mean I/σ(I) obs: 2 / Num. unique all: 48911 / Rsym value: 0.443 / % possible all: 98.6

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Processing

Software
NameVersionClassification
CBASSdata collection
AMoREphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EA6

4ea6


Resolution: 2.1→45.83 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.994 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.037 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26528 2634 5.1 %RANDOM
Rwork0.21425 ---
obs0.21679 48888 97.99 %-
all-98715 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.951 Å2
Baniso -1Baniso -2Baniso -3
1-19.23 Å20 Å20 Å2
2--19.23 Å20 Å2
3----38.46 Å2
Refinement stepCycle: LAST / Resolution: 2.1→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4140 0 111 269 4520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024349
X-RAY DIFFRACTIONr_bond_other_d0.0040.022904
X-RAY DIFFRACTIONr_angle_refined_deg2.0681.9545903
X-RAY DIFFRACTIONr_angle_other_deg1.1083.0037005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6575536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.06424210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.96515622
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6321528
X-RAY DIFFRACTIONr_chiral_restr0.130.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0214933
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02934
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 180 -
Rwork0.376 3320 -
obs--89.49 %

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