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- PDB-1ifp: INOVIRUS (FILAMENTOUS BACTERIOPHAGE) STRAIN PF3 MAJOR COAT PROTEI... -

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Basic information

Entry
Database: PDB / ID: 1ifp
TitleINOVIRUS (FILAMENTOUS BACTERIOPHAGE) STRAIN PF3 MAJOR COAT PROTEIN ASSEMBLY
ComponentsMAJOR COAT PROTEIN ASSEMBLY
KeywordsVIRUS / VIRUS COAT PROTEIN / Helical virus
Function / homology
Function and homology information


helical viral capsid / host cell plasma membrane / membrane
Similarity search - Function
Inovirus Coat protein B / ATP synthase delta/epsilon subunit, C-terminal domain / 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 Pf3 (virus)
MethodFIBER DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsWelsh, L.C. / Symmons, M.F. / Perham, R.N. / Marvin, D.A.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Structure of the capsid of Pf3 filamentous phage determined from X-ray fibre diffraction data at 3.1 A resolution.
Authors: Welsh, L.C. / Symmons, M.F. / Sturtevant, J.M. / Marvin, D.A. / Perham, R.N.
#1: 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.
#2: Journal: Phase Transitions / Year: 1992
Title: Two Forms of Pf1 Inovirus: X-Ray Diffraction Studies on a Structural Phase Transition and a Calculated Libration Normal Mode of the Asymmetric Unit
Authors: Marvin, D.A. / Nave, C. / Bansal, M. / Hale, R.D. / Salje, E.K.H.
#3: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
#4: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Erratum. Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
#5: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
Authors: Marvin, D.A.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...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.process_site / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
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: MAJOR COAT PROTEIN ASSEMBLY


Theoretical massNumber of molelcules
Total (without water)4,6321
Polymers4,6321
Non-polymers00
Water00
1
A: MAJOR COAT PROTEIN ASSEMBLY
x 35


Theoretical massNumber of molelcules
Total (without water)162,13635
Polymers162,13635
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation34
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: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 35 / Rise per n subunits: 2.9 Å / Rotation per n subunits: 65.667 °)

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Components

#1: Protein/peptide MAJOR COAT PROTEIN ASSEMBLY / PF3 INOVIRUS


Mass: 4632.466 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage Pf3 (virus) / Genus: Inovirus / Strain: NEW YORK / Description: FILAMENTOUS BACTERIOPHAGE / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P03623

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
Conc.: 30 mg/ml / Common name: protein

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1995 / Details: MIRRORS
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 3.1→60 Å

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLORrefinement
CCP13(LSQINT)data reduction
CCP13-FDSCALEdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IFN

1ifn


Resolution: 3.1→12 Å / Rfactor Rfree error: 0.01 / Cross valid method: A POSTERIORI
Details: MODEL REFINED WITH A VERSION OF X-PLOR 3.1 MODIFIED FOR USE WITH FIBRE DIFFRACTION DATA BY WANG & STUBBS (1993) ACTA CRYST. A49, 504-513.
RfactorNum. reflection% reflection
Rfree0.39 211 12.2 %
Rwork0.17 --
obs0.17 1734 -
Displacement parametersBiso mean: 19 Å2
Refinement stepCycle: LAST / Resolution: 3.1→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms326 0 0 0 326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT NCS WAS IMPOSED ON THE MODEL THROUGHOUT THE REFINEMENT.
LS refinement shellResolution: 3.1→3.43 Å / Total num. of bins used: 4 /
RfactorNum. reflection
Rwork0.251 112
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.4

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