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- PDB-2lic: NMR Structure of the Polyserine Tract of Apis mellifera Vitelloge... -

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Basic information

Entry
Database: PDB / ID: 2lic
TitleNMR Structure of the Polyserine Tract of Apis mellifera Vitellogenin, residues 358-392
ComponentsVitellogenin
KeywordsLIPID TRANSPORT
Function / homology
Function and homology information


nutrient reservoir activity / lipid transporter activity / extracellular region
Similarity search - Function
Vitellinogen, open beta-sheet / : / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. ...Vitellinogen, open beta-sheet / : / Vitellinogen, open beta-sheet / DUF1943 / Vitellogenin, N-terminal / Lipovitellin-phosvitin complex, superhelical domain / Vitellinogen, beta-sheet N-terminal / Lipid transport protein, beta-sheet shell / Lipoprotein amino terminal region / Vitellogenin domain profile. / Lipoprotein N-terminal Domain / von Willebrand factor, type D domain / von Willebrand factor type D domain / VWFD domain profile. / von Willebrand factor (vWF) type D domain
Similarity search - Domain/homology
Biological speciesApis mellifera (honey bee)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 2
AuthorsHavukainen, H. / Halskau Jr., O.
CitationJournal: J Exp Biol / Year: 2012
Title: A vitellogenin polyserine cleavage site: highly disordered conformation protected from proteolysis by phosphorylation.
Authors: Havukainen, H. / Underhaug, J. / Wolschin, F. / Amdam, G. / Halskau, O.
History
DepositionAug 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitellogenin


Theoretical massNumber of molelcules
Total (without water)4,0661
Polymers4,0661
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Vitellogenin


Mass: 4066.289 Da / Num. of mol.: 1 / Fragment: Vg polyserine tract residues 358-392 / Mutation: S373T / Source method: obtained synthetically / Source: (synth.) Apis mellifera (honey bee) / References: UniProt: Q868N5
Has protein modificationY

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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-1H TOCSY
1312D 1H-1H NOESY

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Sample preparation

DetailsContents: 7.8 w/v [U-15N]-ILE Vg, 0.02 % sodium azide, 50 mM sodium phosphate, 5 % DSS, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
7.8 w/vVg-1[U-15N]-ILE1
0.02 %sodium azide-21
50 mMsodium phosphate-31
5 %DSS-41
Sample conditionsIonic strength: 0.06 / pH: 6.7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AV600 / Manufacturer: Bruker / Model: AV / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA1.2Linge, O'Donoghue and Nilgesdata analysis
ARIA1.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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