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- PDB-6obk: NMR structure of Orf47 from Lactococcus virus P2 -

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Basic information

Entry
Database: PDB / ID: 6obk
TitleNMR structure of Orf47 from Lactococcus virus P2
ComponentsUncharacterized protein ORF47
KeywordsVIRAL PROTEIN
Function / homologyMiddle expressed protein 2
Function and homology information
Biological speciesLactococcus phage p2 (virus)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsGagne, S.M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Fonds de Recherche du Quebec - Nature et Technologies (FRQNT) Canada
CitationJournal: To Be Published
Title: Structure determination of ORF47 from Lactococcus virus P2
Authors: Gagne, S.M.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

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Assembly

Deposited unit
A: Uncharacterized protein ORF47


Theoretical massNumber of molelcules
Total (without water)5,1381
Polymers5,1381
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3810 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide Uncharacterized protein ORF47


Mass: 5137.874 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Lactococcus phage p2 (virus) / References: UniProt: D3WAF4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-1H COSY
121isotropic12D 1H-1H TOCSY
131isotropic12D 1H-1H NOESY
141isotropic12D 1H-15N HSQC
151isotropic12D 1H-13C HSQC

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Sample preparation

DetailsType: solution
Contents: 20 mM potassium phosphate, 50 mM potassium chloride, 90% H2O/10% D2O
Label: unlabeled_1 / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
20 mMpotassium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
Sample conditionsIonic strength: 50 KCl mM / Label: Conditions_1 / pH: 6.3 / Pressure: 1 atm / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxdata analysis
RefinementMethod: torsion angle dynamics / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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