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- PDB-1zn5: Solid State NMR Structure of the low-temperature form of the Pf1 ... -

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Basic information

Entry
Database: PDB / ID: 1zn5
TitleSolid State NMR Structure of the low-temperature form of the Pf1 Major Coat Protein in Magnetically Aligned Bacteriophage
ComponentsCoat protein B
KeywordsVIRUS / alpha-helix / virion / orientational constraints / Helical virus
Function / homology
Function and homology information


helical viral capsid / host cell membrane / membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #230 / Inovirus Coat protein B / Capsid protein G8P / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPseudomonas phage Pf1 (virus)
MethodSOLID-STATE NMR / Determination of torsion angles between adjacent residues using solid-state NMR frequencies
AuthorsThiriot, D.S. / Nevzorov, A.A. / Opella, S.J.
CitationJournal: Protein Sci. / Year: 2005
Title: Structural basis of the temperature transition of Pf1 bacteriophage.
Authors: Thiriot, D.S. / Nevzorov, A.A. / Opella, S.J.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coat protein B


Theoretical massNumber of molelcules
Total (without water)4,6121
Polymers4,6121
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)27 / 100structural fitting of PISEMA spectrum with fixed peptide plane geometry
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Coat protein B / Major coat protein


Mass: 4612.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Host bacteria is Pseudomonas Aeruginosa. / Source: (natural) Pseudomonas phage Pf1 (virus) / Genus: Inovirus / References: UniProt: P03621

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentType: PISEMA
NMR detailsText: MODEL 1 IS THE BASIC SOLID-STATE NMR STRUCTURE (NO SIDECHAINS), WHILE MODELS 2-27 ARE IDENTICAL TRANSLATED AND ROTATED COPIES OF MODEL 1 INCLUDED TO PRESENT THE MODEL OF THE WHOLE BACTERIOPHAGE ASSEMBLY.

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Sample preparation

DetailsContents: Approximately 50 mg/ml Pf1 bacteriophage, u-15N / Solvent system: 5 mM sodium borate buffer
Sample conditionspH: 8 / Pressure: ambient / Temperature: 273 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 750 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2data analysis
Felix2000.1data analysis
Matlab scripts1Nevzorov A.A., Opella, S.J.structure solution
SCWRLBower et al.refinement
RefinementMethod: Determination of torsion angles between adjacent residues using solid-state NMR frequencies
Software ordinal: 1
Details: This is a backbone only model. Constant peptide plane geometry was assumed. Torsion angles phi and psi were allowed to vary within 10-20 degrees relative to phi=-65, psi=-40. Radial and ...Details: This is a backbone only model. Constant peptide plane geometry was assumed. Torsion angles phi and psi were allowed to vary within 10-20 degrees relative to phi=-65, psi=-40. Radial and angular positioning of subunits in a manner similar to and in comparison with structure 1PJF, which involved minimization against published neutron diffraction distance constraints and energy minimization with sidechains using the program SCWRL.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structural fitting of PISEMA spectrum with fixed peptide plane geometry
Conformers calculated total number: 100 / Conformers submitted total number: 27

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