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- PDB-1pjf: Solid State NMR structure of the Pf1 Major Coat Protein in Magnet... -

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Basic information

Entry
Database: PDB / ID: 1pjf
TitleSolid State NMR structure of the Pf1 Major Coat Protein in Magnetically Aligned Bacteriophage
ComponentsCOAT PROTEIN B
KeywordsVIRAL PROTEIN / Helical virus
Function / homologyInovirus Coat protein B / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesPseudomonas phage Pf1 (virus)
MethodSOLID-STATE NMR / CONSTRUCTION OF BACTERIOPHAGE MODEL BASED ON THE SOLID STATE NMR STRUCTURE OF THE MAJOR COAT PROTEIN MONOMER
AuthorsThiriot, D.S. / Nevzorov, A.A. / Zagyanskiy, L. / Wu, C.H. / Opella, S.J.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure of the coat protein in Pf1 bacteriophage determined by solid-state NMR spectroscopy.
Authors: Thiriot, D.S. / Nevzorov, A.A. / Zagyanskiy, L. / Wu, C.H. / Opella, S.J.
History
DepositionJun 2, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 6, 2012Group: Structure summary
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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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 / 116
Representativenearest structure to the average of the 60 best ramachandran structures (based on a statistical ramachandran potential) out of 1000 total structures.

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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: Pseudomonas aeruginosa (ATCC #25102) was the host bacteria.
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 (WITH SIDECHAINS ADDED AND ENERGY MINIMIZED) INCLUDED TO ...Text: MODEL 1 IS THE BASIC SOLID-STATE NMR STRUCTURE (NO SIDECHAINS), WHILE MODELS 2-27 ARE IDENTICAL TRANSLATED AND ROTATED COPIES OF MODEL 1 (WITH SIDECHAINS ADDED AND ENERGY MINIMIZED) INCLUDED TO PRESENT THE MODEL OF THE WHOLE BACTERIOPHAGE ASSEMBLY.

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Sample preparation

DetailsContents: 50 MG/ML PF1 MAJOR COAT PROTEIN, U-15N, 5 MM SODIUM BORATE BUFFER
Sample conditionspH: 8 / Pressure: AMBIENT / Temperature: 303 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
MATLAB SCRIPTS 6.5, SCWRL2.95 (BLUE HORIZON MODIFIED)NEVZOROV, THIRIOT (MATLAB SCRIPTS), BOWER, COHEN, DUNBRACK, MAJUMDAR, CHUKKAPALLI (SCWRL)refinement
Felix2000.1structure solution
XwinNMRstructure solution
MATLAB SCRIPT6.5structure solution
RefinementMethod: CONSTRUCTION OF BACTERIOPHAGE MODEL BASED ON THE SOLID STATE NMR STRUCTURE OF THE MAJOR COAT PROTEIN MONOMER
Software ordinal: 1
Details: SIDECHAINS WERE ADDED TO THE SOLID STATE NMR BACKBONE STRUCTURE USING THE PROGRAM SCWRL. A BACTERIOPHAGE MODEL WAS CONSTRUCTED BY APPLYING PUBLISHED X- RAY FIBER AND NEUTRON DIFFRACTION ...Details: SIDECHAINS WERE ADDED TO THE SOLID STATE NMR BACKBONE STRUCTURE USING THE PROGRAM SCWRL. A BACTERIOPHAGE MODEL WAS CONSTRUCTED BY APPLYING PUBLISHED X- RAY FIBER AND NEUTRON DIFFRACTION SYMMETRY AND DISTANCE CONSTRAINTS (INITIAL PHAGE), WHICH WAS FURTHER REFINED BY COMPARING THE REPULSIVE AMBER ENERGY (USING SCWRL) OF MANY CONFIGURATIONS IN WHICH THE MONOMERS HAD BEEN SYMMETRICALLY ROTATED AND TRANSLATED WITH RESPECT TO THE INITIAL PHAGE.
NMR representativeSelection criteria: nearest structure to the average of the 60 best ramachandran structures (based on a statistical ramachandran potential) out of 1000 total structures.
NMR ensembleConformers calculated total number: 116 / Conformers submitted total number: 27

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