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- PDB-2c0x: MOLECULAR STRUCTURE OF FD FILAMENTOUS BACTERIOPHAGE REFINED WITH ... -

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Basic information

Entry
Database: PDB / ID: 2c0x
TitleMOLECULAR STRUCTURE OF FD FILAMENTOUS BACTERIOPHAGE REFINED WITH RESPECT TO X-RAY FIBRE DIFFRACTION AND SOLID-STATE NMR DATA
ComponentsCOAT PROTEIN B
KeywordsVIRAL PROTEIN / FILAMENTOUS BACTERIOPHAGE / ALPHA-HELIX / MEMBRANE PROTEINS / STRUCTURAL PROTEIN / TRANSMEMBRANE / 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)
MethodSOLID-STATE NMR
Model type detailsMINIMIZED AVERAGE
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.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Structure of the Coat Protein in Fd Filamentous Bacteriophage Particles Determined by Solid-State NMR Spectroscopy
Authors: Zeri, A.C. / Mesleh, M.F. / Nevzorov, A.A. / Opella, S.J.
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 1.2Aug 23, 2017Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.3Jul 29, 2020Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Jan 15, 2025Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Revision 1.6Jan 22, 2025Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list / Item: _pdbx_struct_assembly_gen.oper_expression

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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
Water00
1
A: COAT PROTEIN B
x 51


Theoretical massNumber of molelcules
Total (without water)265,81351
Polymers265,81351
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
point symmetry operation50
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representative
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1), (-1), (1)-80.75
2generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)-80.75
3generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)-80.75
4generate(0.809017, -0.587785), (0.587785, 0.809017), (1)-80.75
5generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)-80.75
6generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)-64.6
7generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)-64.6
8generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)-64.6
9generate(1), (1), (1)-64.6
10generate(0.309017, -0.951057), (0.951057, 0.309017), (1)-64.6
11generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)-48.45
12generate(-1), (-1), (1)-48.45
13generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)-48.45
14generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)-48.45
15generate(0.809017, -0.587785), (0.587785, 0.809017), (1)-48.45
16generate(0.309017, -0.951057), (0.951057, 0.309017), (1)-32.3
17generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)-32.3
18generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)-32.3
19generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)-32.3
20generate(1), (1), (1)-32.3
21generate(0.809017, -0.587785), (0.587785, 0.809017), (1)-16.15
22generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)-16.15
23generate(-1), (-1), (1)-16.15
24generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)-16.15
25generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)-16.15
26generate(1), (1), (1)
27generate(0.309017, -0.951057), (0.951057, 0.309017), (1)
28generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)
29generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)
30generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)
31generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)16.15
32generate(0.809017, -0.587785), (0.587785, 0.809017), (1)16.15
33generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)16.15
34generate(-1), (-1), (1)16.15
35generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)16.15
36generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)32.3
37generate(1), (1), (1)32.3
38generate(0.309017, -0.951057), (0.951057, 0.309017), (1)32.3
39generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)32.3
40generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)32.3
41generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)48.45
42generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)48.45
43generate(0.809017, -0.587785), (0.587785, 0.809017), (1)48.45
44generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)48.45
45generate(-1), (-1), (1)48.45
46generate(-0.809017, 0.587785), (-0.587785, -0.809017), (1)64.6
47generate(0.309017, 0.951057), (-0.951057, 0.309017), (1)64.6
48generate(1), (1), (1)64.6
49generate(0.309017, -0.951057), (0.951057, 0.309017), (1)64.6
50generate(-0.809017, -0.587785), (0.587785, -0.809017), (1)64.6
51generate(-1), (-1), (1)80.75
52generate(-0.309017, 0.951057), (-0.951057, -0.309017), (1)80.75
53generate(0.809017, 0.587785), (-0.587785, 0.809017), (1)80.75
54generate(0.809017, -0.587785), (0.587785, 0.809017), (1)80.75
55generate(-0.309017, -0.951057), (0.951057, -0.309017), (1)80.75
DetailsTHE ASSEMBLY REPRESENTED IN THIS ENTRY HAS REGULAR HELICAL SYMMETRY WITH THE FOLLOWING PARAMETERS: ROTATION PER SUBUNIT (TWIST) = -36.00 DEGREES RISE PER SUBUNIT (HEIGHT) = 16.15 ANGSTROMS IN ADDITION, THERE IS 5-FOLD CIRCULAR SYMMETRY AROUND THE HELIX AXIS

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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.
Production host: ENTEROBACTERIA PHAGE FD (virus) / 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
Has protein modificationN
Sequence detailsY21M MUTANT IN CHAIN

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR

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Processing

NMR ensembleConformers submitted total number: 1

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