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- PDB-5jzr: Solid-state MAS NMR structure of Acinetobacter phage 205 (AP205) ... -

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Basic information

Entry
Database: PDB / ID: 5jzr
TitleSolid-state MAS NMR structure of Acinetobacter phage 205 (AP205) coat protein in assembled capsid particles
ComponentsCoat protein
KeywordsVIRAL PROTEIN / COAT PROTEIN
Function / homologyviral capsid / Coat protein
Function and homology information
Biological speciesAcinetobacter phage AP205 (virus)
MethodSOLID-STATE NMR / torsion angle dynamics
AuthorsJaudzems, K. / Andreas, L.B. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. ...Jaudzems, K. / Andreas, L.B. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. / Wegner, S. / Engelke, F. / Lesage, A. / Emsley, L. / Tars, K. / Herrmann, T. / Pintacuda, G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Structure of fully protonated proteins by proton-detected magic-angle spinning NMR.
Authors: Andreas, L.B. / Jaudzems, K. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. / Wegner, S. / Engelke, F. / Lesage, ...Authors: Andreas, L.B. / Jaudzems, K. / Stanek, J. / Lalli, D. / Bertarello, A. / Le Marchand, T. / Cala-De Paepe, D. / Kotelovica, S. / Akopjana, I. / Knott, B. / Wegner, S. / Engelke, F. / Lesage, A. / Emsley, L. / Tars, K. / Herrmann, T. / Pintacuda, G.
History
DepositionMay 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: pdbx_nmr_exptl_sample_conditions
Item: _pdbx_nmr_exptl_sample_conditions.temperature / _pdbx_nmr_exptl_sample_conditions.temperature_units
Revision 1.4Aug 21, 2019Group: Data collection / Category: pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.5Jun 19, 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: Coat protein
B: Coat protein


Theoretical massNumber of molelcules
Total (without water)28,0462
Polymers28,0462
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area5880 Å2
ΔGint-39 kcal/mol
Surface area16860 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Coat protein


Mass: 14022.842 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter phage AP205 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9AZ42

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic13D HhNH
121isotropic13D HhCH
131isotropic13D (H)CCH-TOCSY
141isotropic13D (H)CCH-TOCSY
151isotropic13D hNCAH
161isotropic13D hNcoCAH
171isotropic13D hCOCAH
191isotropic13D hCOnCAH
181isotropic13D hCANH
1101isotropic13D hcoCAcoNH

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Sample preparation

DetailsType: solid
Contents: 500 mg/mL [U-100% 13C; U-100% 15N] AP205 coat protein, 15 % [U-2H] PEG, 5 mM HEPES, 50 mM sodium chloride, H2O
Label: 0.7 mm / Solvent system: H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
500 mg/mLAP205 coat protein[U-100% 13C; U-100% 15N]1
15 %PEG[U-2H]1
5 mMHEPESnatural abundance1
50 mMsodium chloridenatural abundance1
Sample conditionsIonic strength: 0.055 M / Ionic strength err: 0.05 / Label: solid / pH: 7.5 / Pressure: AMBIENT atm / Temperature: 283 K / Temperature err: 5

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 1000 MHz / Details: Bruker 0.7 mm MAS probe

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Processing

NMR software
NameVersionDeveloperClassification
SparkyGoddardchemical shift assignment
CARA1.9Keller and Wuthrichchemical shift assignment
TopSpin3.5Bruker Biospincollection
SparkyGoddardpeak picking
TopSpin3.5Bruker Biospinprocessing
UNIO2.6Torsten Herrmann et al.structure calculation
CYANA3.97Guntert, Mumenthaler and Wuthrichstructure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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