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- PDB-5lqv: Spatial structure of the lentil lipid transfer protein in complex... -

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Basic information

Entry
Database: PDB / ID: 5lqv
TitleSpatial structure of the lentil lipid transfer protein in complex with anionic lysolipid LPPG
ComponentsNon-specific lipid-transfer protein 2
KeywordsLIPID TRANSPORT / plant defense peptide lipid transfer protein lens culinaris complex with lipid / STRUCTURE FROM CYANA 3.0 / lipid transfer
Function / homology
Function and homology information


lipid transport / lipid binding
Similarity search - Function
Plant lipid transfer proteins signature. / Plant non-specific lipid-transfer protein/Par allergen / Plant lipid-transfer and hydrophobic proteins / Hydrophobic Seed Protein / Protease inhibitor/seed storage/LTP family / Plant lipid transfer protein / seed storage protein / trypsin-alpha amylase inhibitor domain family / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain / Bifunctional inhibitor/plant lipid transfer protein/seed storage helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-PGM / Non-specific lipid-transfer protein 2
Similarity search - Component
Biological speciesLens culinaris (lentil)
MethodSOLUTION NMR / simulated annealing
AuthorsMineev, K.S. / Shenkarev, Z.O. / Arseniev, A.S. / Melnikova, D.N. / Finkina, E.I. / Ovchinnikova, T.V.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Russian Science Foundation14-50-00131 Russian Federation
CitationJournal: Biochemistry / Year: 2017
Title: Ligand Binding Properties of the Lentil Lipid Transfer Protein: Molecular Insight into the Possible Mechanism of Lipid Uptake.
Authors: Shenkarev, Z.O. / Melnikova, D.N. / Finkina, E.I. / Sukhanov, S.V. / Boldyrev, I.A. / Gizatullina, A.K. / Mineev, K.S. / Arseniev, A.S. / Ovchinnikova, T.V.
History
DepositionAug 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific lipid-transfer protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7832
Polymers9,3001
Non-polymers4841
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area1030 Å2
ΔGint-11 kcal/mol
Surface area5470 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Non-specific lipid-transfer protein 2 / LTP2


Mass: 9299.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil) / Production host: Escherichia coli (E. coli) / References: UniProt: A0AT29
#2: Chemical ChemComp-PGM / 1-MYRISTOYL-2-HYDROXY-SN-GLYCERO-3-[PHOSPHO-RAC-(1-GLYCEROL)] / LYSOPHOSPHATIDYLGLYCEROL


Mass: 483.553 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H44O9P

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D 1H-13C NOESY aliphatic
121isotropic13D (H)CCH-TOCSY
131isotropic13D HN(CA)CB
141isotropic13D 1H-15N NOESY
151isotropic113C-filtered NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 0.3 mM [U-99% 13C; U-99% 15N] LTP2, 2 mM LPPG, 20 mM sodium acetate, 0.01 % sodium azide, 90% H2O/10% D2O
Label: 1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMLTP2[U-99% 13C; U-99% 15N]1
2 mMLPPGnatural abundance1
20 mMsodium acetatenatural abundance1
0.01 %sodium azidenatural abundance1
Sample conditionsIonic strength: 20 mM / Label: 1 / pH: 5.6 / Pressure: 1 bar / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker AvanceIII / Manufacturer: Bruker / Model: AvanceIII / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure calculation
CARA1.9.1Keller and Wuthrichchemical shift assignment
TopSpinBruker Biospinprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 200 / Conformers submitted total number: 20

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