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- PDB-2mal: Solution structure of Lipid Transfer Protein from Lentil Lens Cul... -

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Basic information

Entry
Database: PDB / ID: 2mal
TitleSolution structure of Lipid Transfer Protein from Lentil Lens Culinaris
ComponentsNon-specific lipid-transfer protein 2
KeywordsLIPID TRANSPORT / plant lipid transfer protein / Lens Culinaris
Function / homology
Function and homology information


lipid transport / lipid binding / membrane
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 2
Similarity search - Component
Biological speciesLens culinaris (lentil)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsGizatullina, A.K. / Mineev, K.S. / Shenkarev, Z.O.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Recombinant production and solution structure of lipid transfer protein from lentil Lens culinaris.
Authors: Gizatullina, A.K. / Finkina, E.I. / Mineev, K.S. / Melnikova, D.N. / Bogdanov, I.V. / Telezhinskaya, I.N. / Balandin, S.V. / Shenkarev, Z.O. / Arseniev, A.S. / Ovchinnikova, T.V.
History
DepositionJul 16, 2013Deposition site: BMRB / Processing site: RCSB
SupersessionOct 2, 2013ID: 2LJO
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2013Group: Database references
Revision 1.2Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,3001
Polymers9,3001
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 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Non-specific lipid-transfer protein 2 / LTP2 / Non-specific lipid-transfer protein 7 / LTP7


Mass: 9299.694 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lens culinaris (lentil) / Plasmid: pET-His8-TrxL-Lc-LTP2 / Production host: Escherichia coli (E. coli) / References: UniProt: A0AT29

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D DQF-COSY
1212D 1H-1H TOCSY
1312D 1H-1H NOESY
1422D 1H-15N HSQC
1523D 1H-15N NOESY
1623D 1H-15N TOCSY
1723D HNHA
1823D HNHB
1933D 1H-13C NOESY
11033D (H)CCH-TOCSY
11133D 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4 mM [U-100% 15N] Lc-LTP2, 100% D2O100% D2O
21.4 mM [U-100% 15N] Lc-LTP2, 95% H2O/5% D2O95% H2O/5% D2O
31.0-1.5 mM [U-100% 13C; U-100% 15N] Lc-LTP2, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
1.4 mMLc-LTP2-1[U-100% 15N]1
1.4 mMLc-LTP2-2[U-100% 15N]2
mMLc-LTP2-3[U-100% 13C; U-100% 15N]1.0-1.53
Sample conditionsIonic strength: 0 / pH: 5.6 / 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
NameDeveloperClassification
XEASYKeller and Wuthrichpeak picking
XEASYKeller and Wuthrichchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichdata analysis
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
TALOSCornilescu, Delaglio and Baxrefinement
ProcheckLaskowski, MacArthur, Smith, Jones, Hutchinson, Morris, Moss and Thorefinement
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 817 / NOE intraresidue total count: 290 / NOE long range total count: 79 / NOE medium range total count: 240 / NOE sequential total count: 208
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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