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- PDB-2n81: Solution Structure of Lipid Transfer Protein From Pea Pisum Sativum -

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Basic information

Entry
Database: PDB / ID: 2n81
TitleSolution Structure of Lipid Transfer Protein From Pea Pisum Sativum
ComponentsLipid Transfer Protein
KeywordsLIPID BINDING PROTEIN / ANTIMICROBIAL PROTEIN / ALLERGEN / lipid binding / antimicrobial activity
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
Non-specific lipid-transfer protein
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsParamonov, A.S. / Rumynskiy, E.I. / Bogdanov, I.V. / Finkina, E.I. / Melnikova, D.N. / Ovchinnikova, T.V. / Shenkarev, Z.O. / Arseniev, A.S.
CitationJournal: BMC Plant Biol
Title: A novel lipid transfer protein from the pea Pisum sativum: isolation, recombinant expression, solution structure, antifungal activity, lipid binding, and allergenic properties.
Authors: Bogdanov, I.V. / Shenkarev, Z.O. / Finkina, E.I. / Melnikova, D.N. / Rumynskiy, E.I. / Arseniev, A.S. / Ovchinnikova, T.V.
History
DepositionSep 30, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2017Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipid Transfer Protein


Theoretical massNumber of molelcules
Total (without water)9,5461
Polymers9,5461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 300target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Lipid Transfer Protein / Ps-LTP1


Mass: 9545.999 Da / Num. of mol.: 1 / Mutation: M11L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pisum sativum (garden pea) / Variant: Sacharniy 2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): Star(DE3) / References: UniProt: A0A182DV18*PLUS

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D HN(CA)CB
1613D 1H-15N NOESY
1713D 1H-13C NOESY aliphatic
1813D 1H-15N TOCSY
1913D (H)CCH-TOCSY
11013D HN(CO)CA

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] PS-LTP1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1 mM / Component: PS-LTP1-1 / Isotopic labeling: [U-98% 13C; U-98% 15N]
Sample conditionsIonic strength: 10 / pH: 5.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: Avance / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CARA1.8Keller and Wuthrichchemical shift assignment
CARA1.8Keller and Wuthrichpeak picking
CARA1.8Keller and Wuthrichchemical shift calculation
TOPSPIN2.1Bruker Biospincollection
TOPSPIN2.1Bruker Biospinprocessing
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA1.8Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 300 / Conformers submitted total number: 20

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