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- PDB-1mzt: NMR structure of the fd bacteriophage pVIII coat protein in lipid... -

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Basic information

Entry
Database: PDB / ID: 1mzt
TitleNMR structure of the fd bacteriophage pVIII coat protein in lipid bilayer membranes
Componentsmajor coat protein pVIII
KeywordsVIRAL PROTEIN / fd coat protein / membrane-bound / pVIII
Function / homologyPhage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / Capsid protein G8P / helical viral capsid / host cell membrane / membrane / Capsid protein G8P
Function and homology information
Biological speciesEnterobacteria phage fd (virus)
MethodSOLID-STATE NMR / Calculation of bond orientations, dihedral angles from solid-state NMR restraints, back-calculation of NMR data from oriented structure
AuthorsMarassi, F.M. / Opella, S.J.
Citation
Journal: Protein Sci. / Year: 2003
Title: Simultaneous assignment and structure determination of a membrane protein from NMR orientational restraints
Authors: Marassi, F.M. / Opella, S.J.
#1: Journal: J.Biomol.NMR / Year: 2002
Title: Using Pisa pies to resolve ambiguities in angular constraints from PISEMA spectra of aligned proteins
Authors: Marassi, F.M. / Opella, S.J.
History
DepositionOct 9, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE AUTHOR PROVIDED COORDINATES FOR THE PROTEIN BACKBONE ONLY.

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: major coat protein pVIII


Theoretical massNumber of molelcules
Total (without water)5,2441
Polymers5,2441
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)1 / 6structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide major coat protein pVIII / Filamentous phage cloning vector fd-tet


Mass: 5244.000 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage fd (virus) / Genus: Inovirus / Species: Enterobacteria phage M13 / References: UniProt: P69539

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experimentType: 1H/15N PISEMA
NMR detailsText: The structure was determined from one uniformly and four selectively 15N-labeled samples.

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Sample preparation

DetailsContents: 8 mg 15N-labeled fd coat protein, 64 mg POPC, 16 mg POPG, lipid bilayers oriented on glass slides
Solvent system: Lipid bilayers hydrated in water
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 296 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Chemagnetics CMX / Manufacturer: Chemagnetics / Model: CMX / Field strength: 400 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CMXW95Chemagneticscollection
Felix95Biosymdata analysis
BACKTOR2Marassi, Opellastructure solution
BACKTOR2Marassi, Opellarefinement
RefinementMethod: Calculation of bond orientations, dihedral angles from solid-state NMR restraints, back-calculation of NMR data from oriented structure
Software ordinal: 1
Details: Structure calculated from 40 chemical shift and 40 dipolar coupling restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 6 / Conformers submitted total number: 1

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