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- PDB-6m56: Solution NMR Structure of Peptide P9R -

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Basic information

Entry
Database: PDB / ID: 6m56
TitleSolution NMR Structure of Peptide P9R
ComponentsPeptide P9R
KeywordsANTIVIRAL PROTEIN
Function / homology
Function and homology information


Defensins / Beta defensins / CCR6 chemokine receptor binding / chemoattractant activity / cell chemotaxis / chemotaxis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / extracellular space
Similarity search - Function
Beta defensin type / Beta defensin
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsYuen, K.Y. / Zhao, H.J. / Yung, T.M. / Sze, K.H.
CitationJournal: Nat Commun / Year: 2020
Title: A broad-spectrum virus- and host-targeting peptide against respiratory viruses including influenza virus and SARS-CoV-2.
Authors: Zhao, H. / To, K.K.W. / Sze, K.H. / Yung, T.T. / Bian, M. / Lam, H. / Yeung, M.L. / Li, C. / Chu, H. / Yuen, K.Y.
History
DepositionMar 10, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide P9R


Theoretical massNumber of molelcules
Total (without water)3,4181
Polymers3,4181
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein/peptide Peptide P9R / Beta-defensin 4 / mBD-4 / Defensin / beta 4


Mass: 3418.084 Da / Num. of mol.: 1 / Mutation: H21R/K23R/K28R / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P82019

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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
142isotropic12D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution11 mg/mL NA- P9R, 95% H2O/5% D2O1 mg/mL P9R dissolved in pure 95% H2O/5% D2O.5% D2O95% H2O/5% D2O
solution21 mg/mL NA- P9R, 100% D2O1 mg/mL P9R dissolved in pure 99.996% D2O.100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mg/mLP9RNA-1
1 mg/mLP9RNA-2
Sample conditionsIonic strength: 0 Not defined / Label: Standard / pH: 7 / Pressure: 1 atm / Temperature: 298.15 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 700 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.21Brunger A. T. et.al.refinement
ARIA2.3Linge, O'Donoghue and Nilgesstructure calculation
CcpNmr Analysis2.4.2CCPNchemical shift assignment
DANGLE1.1Nicole Cheung, Tim Stevens, Bill Broadhurststructure calculation
TopSpin4.0.6Bruker Biospincollection
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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