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- PDB-7app: Structure of Lipase TL from capillary grown crystal in the presen... -

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Basic information

Entry
Database: PDB / ID: 7app
TitleStructure of Lipase TL from capillary grown crystal in the presence of agarose
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
FORMIC ACID / Lipase
Similarity search - Component
Biological speciesThermomyces lanuginosus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 13, 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

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Assembly

Deposited unit
A: Lipase
B: Lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,88722
Polymers58,6852
Non-polymers1,20220
Water8,647480
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-41 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.851, 137.851, 79.942
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 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
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 480 / Source method: isolated from a natural source / Formula: H2O
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: 3.62 Å3/Da / Density % sol: 66 % / Description: Hexagonal bipyramid
Crystal growTemperature: 293 K / Method: counter-diffusion / pH: 7
Details: 5.0 M NaFormate, 0.1 M Tris HCl, 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 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.571
11-K, -H, -L20.429
ReflectionResolution: 1.7→68.93 Å / Num. obs: 94343 / % possible obs: 100 % / Redundancy: 18.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.153 / Rpim(I) all: 0.036 / Rrim(I) all: 0.157 / Net I/σ(I): 12.7 / Num. measured all: 1738317 / Scaling rejects: 3359
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7316.40.85946510.8650.2180.886100
9.33-68.9316.70.096140.9960.0210.09299.8

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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: 1.7→66.42 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 0.954 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.013 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1544 4792 5.1 %RANDOM
Rwork0.127 ---
obs0.1284 89507 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.69 Å2 / Biso mean: 23.314 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-8.14 Å20 Å20 Å2
2--8.14 Å20 Å2
3----16.28 Å2
Refinement stepCycle: final / Resolution: 1.7→66.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4142 0 76 480 4698
Biso mean--42.2 35.75 -
Num. residues----537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0134869
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174261
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.6526675
X-RAY DIFFRACTIONr_angle_other_deg1.5741.5929916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.245646
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17621.844282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02115740
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7631540
X-RAY DIFFRACTIONr_chiral_restr0.1080.2627
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.025919
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021141
LS refinement shellResolution: 1.704→1.748 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.193 360 -
Rwork0.15 6589 -
all-6949 -
obs--99.87 %

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