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- PDB-7apn: Structure of Lipase TL from bulk agarose grown crystal -

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Basic information

Entry
Database: PDB / ID: 7apn
TitleStructure of Lipase TL from bulk agarose grown crystal
ComponentsLipase
KeywordsHYDROLASE / Lipase / Reinforced Crosslinked Lipase crystals / CLECs
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
PHOSPHATE ION / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGavira, J.A. / Martinez-Rodriguez, S. / Fernande-Penas, R. / Verdugo-Escamilla, C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesBIO2016-74875-P Spain
CitationJournal: Cryst.Growth Des. / Year: 2021
Title: Production of Cross-Linked Lipase Crystals at a Preparative Scale.
Authors: Fernandez-Penas, R. / Verdugo-Escamilla, C. / Martinez-Rodriguez, S. / Gavira, J.A.
History
DepositionOct 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,64211
Polymers58,6852
Non-polymers9579
Water7,494416
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-36 kcal/mol
Surface area21790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.187, 141.187, 80.234
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermomyces lanuginosus (fungus) / Gene: LIP / Production host: Aspergillus sp. (mold) / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 , 4 types, 423 molecules

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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 1.9 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7 / Details: 0,1M KNa-phosphate, agarose 0,2% (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→122.27 Å / Num. obs: 61405 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.066 / Rrim(I) all: 0.176 / Net I/σ(I): 8.2 / Num. measured all: 425687 / Scaling rejects: 634
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.057.30.9683326445710.660.3781.0421.9100
8.94-122.276.30.08545867310.9910.0360.09219.499.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6hw1

6hw1


Resolution: 2→122.27 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.013 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2504 3038 5 %RANDOM
Rwork0.2129 ---
obs0.2147 58328 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111 Å2 / Biso mean: 33.718 Å2 / Biso min: 17.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20.42 Å20 Å2
2--0.84 Å20 Å2
3----2.72 Å2
Refinement stepCycle: final / Resolution: 2→122.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 58 416 4616
Biso mean--57.9 42.65 -
Num. residues----538
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134651
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174088
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.6536369
X-RAY DIFFRACTIONr_angle_other_deg1.3341.5889502
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0175602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.3921.868273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95715708
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9571538
X-RAY DIFFRACTIONr_chiral_restr0.0730.2598
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025514
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021068
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 221 -
Rwork0.311 4345 -
all-4566 -
obs--100 %

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