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- PDB-2n2z: NMR spatial structure of nonspecific lipid transfer protein from ... -

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Basic information

Entry
Database: PDB / ID: 2n2z
TitleNMR spatial structure of nonspecific lipid transfer protein from the dill Anethum graveolens L.
ComponentsNon-specific lipid-transfer protein
KeywordsPLANT PROTEIN / lipid transfer protein / plant defense protein
Function / homology
Function and homology information


lipid transport / defense response to fungus / killing of cells of another organism / 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 speciesAnethum graveolens (dill)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsMineev, K.S. / Melnikova, D.N. / Finkina, E.I. / Arseniev, A.S. / Ovchinnikova, T.V.
CitationJournal: J.Pept.Sci. / Year: 2016
Title: A novel lipid transfer protein from the dill Anethum graveolens L.: isolation, structure, heterologous expression, and functional characteristics.
Authors: Melnikova, D.N. / Mineev, K.S. / Finkina, E.I. / Arseniev, A.S. / Ovchinnikova, T.V.
History
DepositionMay 19, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-specific lipid-transfer protein


Theoretical massNumber of molelcules
Total (without water)9,5411
Polymers9,5411
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)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Non-specific lipid-transfer protein


Mass: 9541.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anethum graveolens (dill) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0B4JDK1

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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 aliphatic
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D HNCA
1613D HNCO
1713D HN(CO)CA
1813D HNHA
1913D 1H-15N NOESY
11013D (H)CCH-TOCSY
11113D 1H-13C NOESY aliphatic
11213D (H)CCH-COSY
11313D HNHB

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] protein, 20 mM sodium phosphate, 10 mM glycerol, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMentity-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
10 mMglycerol-31
Sample conditionsIonic strength: 20 / pH: 6.0 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CYANA3Guntert, Mumenthaler and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
qMDD2.5Orekhov and Mayzelprocessing
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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