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- PDB-2c0w: Molecular Structure of fd Filamentous Bacteriophage Refined with ... -

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Basic information

Entry
Database: PDB / ID: 2c0w
TitleMolecular Structure of fd Filamentous Bacteriophage Refined with Respect to X-ray Fibre Diffraction
ComponentsCOAT PROTEIN B
KeywordsVIRUS / CAPSID PROTEIN / FILAMENTOUS BACTERIOPHAGE / MEMBRANE PROTEIN / STRUCTURAL PROTEIN / 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 - #80 / Phage major coat protein, Gp8 / Bacteriophage M13, G8P, capsid domain superfamily / 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 speciesENTEROBACTERIA PHAGE FD (virus)
MethodFIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMarvin, D.A. / Welsh, L.C. / Symmons, M.F. / Scott, W.R.P. / Straus, S.K.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Molecular Structure of Fd (F1, M13) Filamentous Bacteriophage Refined with Respect to X-Ray Fibre Diffraction and Solid-State NMR Data Supports Specific Models of Phage Assembly at the Bacterial Membrane.
Authors: Marvin, D.A. / Welsh, L.C. / Symmons, M.F. / Scott, W.R.P. / Straus, S.K.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Molecular Models and Structural Comparisons of Native and Mutant Class I Filamentous Bacteriophages Ff (Fd, F1, M13), If1 and Ike
Authors: Marvin, D.A. / Hale, R.D. / Nave, C. / Helmer-Citterich, M.
#2: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
#3: Journal: J.Mol.Biol. / Year: 1995
Title: Matching Electrostatic Charge between DNA and Coat Protein in Filamentous Bacteriophage. Fibre Diffraction of Charge-Deletion Mutants.
Authors: Symmons, M.F. / Welsh, L.C. / Nave, C. / Marvin, D.A. / Perham, R.N.
History
DepositionSep 8, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2May 1, 2013Group: Data collection / Source and taxonomy / Structure summary
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _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: COAT PROTEIN B


Theoretical massNumber of molelcules
Total (without water)5,2121
Polymers5,2121
Non-polymers00
Water0
1
A: COAT PROTEIN B
x 55


Theoretical massNumber of molelcules
Total (without water)286,66155
Polymers286,66155
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation54
identity operation1_555x,y,z1
2


  • Idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
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
SymmetryHelical symmetry: (Circular symmetry: 5 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 55 / Rise per n subunits: 16.15 Å / Rotation per n subunits: -36 °)

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Components

#1: Protein/peptide COAT PROTEIN B / FD GENE 8 COAT PROTEIN / MAJOR COAT PROTEIN


Mass: 5212.021 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE FD (virus)
Description: H. HOFFMANN-BERLING Z. NATURFORSCH. SECT. B BIOSCI. V18 P876, Y1963
Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P69539
Compound detailsRESIDUE IN CHAIN A, TYR 44 TO MET WAS AN INTENTIONAL MUTATION IN THE VIRAL GENOME, THIS MUTATION IS ...RESIDUE IN CHAIN A, TYR 44 TO MET WAS AN INTENTIONAL MUTATION IN THE VIRAL GENOME, THIS MUTATION IS KNOWN TO IMPROVE ORIENTATION FOR XRAY STUDIES. THE VIRUS WAS THEN GROWN IN THE NORMAL WAY, NOT USING RECOMBINANT METHODS, SEE REFERENCE 1
Sequence detailsY21M MUTANT IN CHAIN

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS
RadiationMonochromator: GE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3.2→44 Å / Num. obs: 0 / % possible obs: 94 % / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
X-PLORFX-PLOR 3.840refinement
CCP13(LSQINT)data reduction
CCP13-FDSCALEdata scaling
FX-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IFJ

1ifj


Resolution: 3.2→20 Å / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.21 --
obs0.21 826 0 %
Displacement parametersBiso mean: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms366 0 0 0 366
Refine LS restraints
Refine-IDTypeDev ideal
FIBER DIFFRACTIONx_bond_d0.006
FIBER DIFFRACTIONx_bond_d_na
FIBER DIFFRACTIONx_bond_d_prot
FIBER DIFFRACTIONx_angle_d
FIBER DIFFRACTIONx_angle_d_na
FIBER DIFFRACTIONx_angle_d_prot
FIBER DIFFRACTIONx_angle_deg1
FIBER DIFFRACTIONx_angle_deg_na
FIBER DIFFRACTIONx_angle_deg_prot
FIBER DIFFRACTIONx_dihedral_angle_d
FIBER DIFFRACTIONx_dihedral_angle_d_na
FIBER DIFFRACTIONx_dihedral_angle_d_prot
FIBER DIFFRACTIONx_improper_angle_d
FIBER DIFFRACTIONx_improper_angle_d_na
FIBER DIFFRACTIONx_improper_angle_d_prot
FIBER DIFFRACTIONx_mcbond_it
FIBER DIFFRACTIONx_mcangle_it
FIBER DIFFRACTIONx_scbond_it
FIBER DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARALLHDG.PRO VERSION 4.05 / Topol file: TOPALLHDG.PRO VERSION 4.01

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