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- PDB-1ifm: TWO FORMS OF PF1 INOVIRUS: X-RAY DIFFRACTION STUDIES ON A STRUCTU... -

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Basic information

Entry
Database: PDB / ID: 1ifm
TitleTWO FORMS OF PF1 INOVIRUS: X-RAY DIFFRACTION STUDIES ON A STRUCTURAL PHASE TRANSITION AND A CALCULATED LIBRATION NORMAL MODE OF THE ASYMMETRIC UNIT
ComponentsINOVIRUS
KeywordsVIRUS / 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 - #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 / Resolution: 3.3 Å
AuthorsMarvin, D.A.
Citation
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.
#1: Journal: Int.J.Biol.Macromol. / Year: 1990
Title: Model-Building Studies of Inovirus: Genetic Variations on a Geometric Theme
Authors: Marvin, D.A.
#2: Journal: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
Authors: Marvin, D.A.
#3: Journal: J.Mol.Biol. / Year: 1987
Title: Pf1 Inovirus. Electron Density Distribution Calculated by a Maximum Entropy Algorithm from Native Fiber Diffraction Data to 3 Angstroms Resolution and Single Isomorphous Replacement Data to 5 Angstroms Resolution
Authors: Marvin, D.A. / Bryan, R.K. / Nave, C.
#4: Journal: J.Mol.Biol. / Year: 1981
Title: Pf1 Filamentous Bacterial Virus. X-Ray Fibre Diffraction Analysis of Two Heavy-Atom Derivatives
Authors: Nave, C. / Brown, R.S. / Fowler, A.G. / Ladner, J.E. / Marvin, D.A. / Provencher, S.W. / Tsugita, A. / Armstrong, J. / Perham, R.N.
#5: Journal: J.Mol.Biol. / Year: 1974
Title: Filamentous Bacterial Viruses Xi. Molecular Architecture of the Class II (Pf1, Xf) Virion
Authors: Marvin, D.A. / Wiseman, R.L. / Wachtel, E.J.
History
DepositionJan 31, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOVIRUS


Theoretical massNumber of molelcules
Total (without water)4,6121
Polymers4,6121
Non-polymers00
Water00
1
A: INOVIRUS
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 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: 3.05 Å / Rotation per n subunits: 65.915 °)

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Components

#1: Protein/peptide INOVIRUS


Mass: 4612.393 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage Pf1 (virus) / Genus: Inovirus / Strain: PF1 MAJOR / References: UniProt: P03621

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: other / Details: fiber diffraction

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Data collection

Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: EREF / Classification: refinement
RefinementHighest resolution: 3.3 Å
Details: THE MODEL IS REFINED USING THE JACK-LEVITT METHOD (M. LEVITT, J.MOL.BIOL. V. 82, 393, 1974; J.MOL.BIOL. V. 168, 595, 1983; A. JACK, M. LEVITT, ACTA CRYSTALLOG. V. A34, 931, 1978). SEE 1IFD ...Details: THE MODEL IS REFINED USING THE JACK-LEVITT METHOD (M. LEVITT, J.MOL.BIOL. V. 82, 393, 1974; J.MOL.BIOL. V. 168, 595, 1983; A. JACK, M. LEVITT, ACTA CRYSTALLOG. V. A34, 931, 1978). SEE 1IFD FOR DETAILS. THE INDEXING OF UNITS ALONG THE BASIC HELIX IS ILLUSTRATED IN REFERENCE 2. TO GENERATE COORDINATES X(K), Y(K), Z(K) OF UNIT K FROM THE GIVEN COORDINATES X(0), Y(0), Z(0) OF UNIT 0 IN A UNIT CELL WITH HELIX PARAMETERS (TAU, P) = (66.667, 2.90), APPLY THE MATRIX AND VECTOR: | COS(TAU*K) -SIN(TAU*K) 0 | | 0 | | SIN(TAU*K) COS(TAU*K) 0 | + | 0 | | 0 0 1 | | P*K | THE NEIGHBORS IN CONTACT WITH UNIT 0 ARE UNITS K = +/-1, +/-5, +/-6, +/-11 AND +/-17. THESE SYMMETRY-RELATED COPIES ARE USED TO DETERMINE INTERCHAIN NON-BONDED CONTACTS DURING THE REFINEMENT. THE TEMPERATURE FACTOR WAS NOT REFINED AND IS GIVEN THE ARBITRARY VALUE OF 10.
Refinement stepCycle: LAST / Highest resolution: 3.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms322 0 0 0 322

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