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- PDB-2xkm: Consensus structure of Pf1 filamentous bacteriophage from X-ray f... -

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Basic information

Entry
Database: PDB / ID: 2xkm
TitleConsensus structure of Pf1 filamentous bacteriophage from X-ray fibre diffraction and solid-state NMR
ComponentsCAPSID PROTEIN G8P
KeywordsVIRAL PROTEIN / CAPSID PROTEIN / TRANSMEMBRANE / VIRION / VIRUS COAT PROTEIN
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)
MethodFIBER DIFFRACTION / SOLID-STATE NMR / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsStraus, S.K. / P Scott, W.R. / Schwieters, C.D. / Marvin, D.A.
Citation
Journal: Eur.Biophys.J. / Year: 2011
Title: Consensus Structure of Pf1 Filamentous Bacteriophage from X-Ray Fibre Diffraction and Solid-State NMR.
Authors: Straus, S.K. / Scott, W.R. / Schwieters, C.D. / Marvin, D.A.
#1: Journal: Protein Sci. / Year: 2005
Title: Structural Basis of the Temperature Transition of Pf1 Bacteriophage.
Authors: Thiriot, D.S. / Nevzorov, A.A. / Opella, S.J.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1995
Title: Pf1 Filamentous Bacteriophage: Refinement of a Molecular Model by Simulated Annealing Using 3.3 A Resolution X-Ray Fibre Diffraction Data.
Authors: Gonzalez, A. / Nave, C. / Marvin, D.A.
#3: Journal: Eur.Biophys.J. / Year: 2008
Title: The Hand of the Filamentous Bacteriophage Helix.
Authors: Straus, S.K. / Scott, W.R.P. / Marvin, D.A.
#4: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions.
Authors: Marvin, D.A.
History
DepositionJul 9, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Data collection / Database references ...Data collection / Database references / Other / Version format compliance
Revision 1.2Sep 18, 2019Group: Data collection / Category: reflns
Item: _reflns.pdbx_Rmerge_I_obs / _reflns.percent_possible_obs
Revision 1.3Apr 28, 2021Group: Data collection / Other / Category: pdbx_database_status / reflns
Item: _pdbx_database_status.status_code_mr / _pdbx_database_status.status_code_sf / _reflns.pdbx_redundancy
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CAPSID PROTEIN G8P


Theoretical massNumber of molelcules
Total (without water)4,6121
Polymers4,6121
Non-polymers00
Water00
1
A: CAPSID PROTEIN G8P
x 35


Theoretical massNumber of molelcules
Total (without water)161,43435
Polymers161,43435
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation34
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)1.000, 1.000, 1.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number1
Space group name H-MP1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 35 / Rise per n subunits: 3.05 Å / Rotation per n subunits: 65.915 °)
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = 65.915 DEGREES RISE PER SUBUNIT (HEIGHT) = 3.05 ANGSTROMS COORDINATES ARE GIVEN FOR A SINGLE ASYMMETRIC UNIT OF THE COAT PROTEIN ASSEMBLY. THE COMPLETE PROTEIN ASSEMBLY CONTAINS SEVERAL THOUSAND ASYMMETRIC UNITS; THE EXACT NUMBER DEPENDS ON THE LENGTH OF THE DNA. THE PROTEIN ASSEMBLY FORMS A CYLINDRICAL SHELL SURROUNDING A DNA CORE.

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Components

#1: Protein/peptide CAPSID PROTEIN G8P / MAJOR COAT PROTEIN / GENE 8 PROTEIN / G8P / COAT PROTEIN B / PF1 PHAGE COAT PROTEIN GENE 8


Mass: 4612.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 37-82 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS PHAGE PF1 (virus) / References: UniProt: P03621

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Experimental details

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Experiment

Experiment
Method
FIBER DIFFRACTION
SOLID-STATE NMR

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Sample preparation

CrystalDescription: NONE

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→12 Å / Num. obs: 3548 / Observed criterion σ(I): 0.8

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Processing

SoftwareName: XPLOR-NIH / Classification: phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4IFM

4ifm


Highest resolution: 3.3 Å
Refinement stepCycle: LAST / Highest resolution: 3.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms322 0 0 0 322
NMR ensembleConformers submitted total number: 1

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