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- PDB-2ifn: PF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY... -

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Basic information

Entry
Database: PDB / ID: 2ifn
TitlePF1 FILAMENTOUS BACTERIOPHAGE: REFINEMENT OF A MOLECULAR MODEL BY SIMULATED ANNEALING USING 3.3 ANGSTROMS RESOLUTION X-RAY FIBRE DIFFRACTION DATA
ComponentsPF1 FILAMENTOUS BACTERIOPHAGE
KeywordsVIRUS / VIRUS COAT 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 - #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: 4 Å
AuthorsMarvin, D.A.
Citation
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.
#1: 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.
#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: Int.J.Biol.Macromol. / Year: 1989
Title: Dynamics of Telescoping Inovirus: A Mechanism for Assembly at Membrane Adhesions
Authors: Marvin, D.A.
History
DepositionJan 16, 1994Processing site: BNL
Revision 1.0Jan 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 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

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Assembly

Deposited unit
A: PF1 FILAMENTOUS BACTERIOPHAGE


Theoretical massNumber of molelcules
Total (without water)4,6121
Polymers4,6121
Non-polymers00
Water00
1
A: PF1 FILAMENTOUS BACTERIOPHAGE
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: 2.9 Å / Rotation per n subunits: 66.667 °)
DetailsCOORDINATES 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 PF1 FILAMENTOUS BACTERIOPHAGE / PF1 INOVIRUS


Mass: 4612.393 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GROWN IN PSEUDOMONAS AERUGINOSA / Source: (natural) Pseudomonas phage Pf1 (virus) / Genus: Inovirus / References: UniProt: P03621

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Experimental details

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Experiment

ExperimentMethod: FIBER DIFFRACTION

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Processing

Software
NameClassification
X-PLORmodel building
EREFrefinement
X-PLORrefinement
X-PLORphasing
RefinementHighest resolution: 4 Å
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms322 0 0 0 322

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