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- PDB-2bpa: ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND... -

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Basic information

Entry
Database: PDB / ID: 2bpa
TitleATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS
Components
  • (PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)) x 3
  • DNA (5'-D(*AP*AP*AP*AP*C)-3')
KeywordsVirus/DNA / PROTEIN-DNA COMPLEX / SINGLE STRAND / Icosahedral virus / Virus-DNA COMPLEX
Function / homology
Function and homology information


symbiont-mediated perturbation of host process / T=1 icosahedral viral capsid / viral capsid / host cell cytoplasm / symbiont entry into host cell / virion attachment to host cell / structural molecule activity / DNA binding
Similarity search - Function
Microvirus J protein-like / Microvirus J protein / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus ...Microvirus J protein-like / Microvirus J protein / Bacteriophage G4 Capsid Proteins Gpf, Gpg, Gpj, subunit 1 / Microviridae F protein / Major spike protein G / Major spike protein (G protein) / Microviridae F protein / Microviridae F protein superfamily / Capsid protein (F protein) / Capsid/spike protein, ssDNA virus / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
DNA / Capsid protein F / Major spike protein G / DNA-binding protein J
Similarity search - Component
Biological speciesEnterobacteria phage phiX174 (virus)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsMcKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Krishnaswamy, S. / Rossmann, M.G. / Olson, N.H. / Baker, T.S. / Incardona, N.L.
Citation
Journal: Nature / Year: 1992
Title: Atomic structure of single-stranded DNA bacteriophage phi X174 and its functional implications.
Authors: McKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Krishnaswamy, S. / Rossmann, M.G. / Olson, N.H. / Baker, T.S. / Incardona, N.L.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure Determination of the Bacteriophage PhiX174
Authors: McKenna, R. / Xia, D. / Willingmann, P. / Ilag, L.L. / Rossmann, M.G.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Analysis of the Single-Stranded DNA Bacteriophage PhiX174 Refined at a Resolution of 3.0 A
Authors: McKenna, R. / Ilag, L.L. / Rossmann, M.G.
#3: Journal: J.Mol.Biol. / Year: 1990
Title: Preliminary Investigation of the Phage PhiX174
Authors: Willingmann, P. / Krishnaswamy, S. / McKenna, R. / Smith, T.J. / Olson, N.H. / Rossmann, M.G. / Stow, P.L. / Incardona, N.L.
#4: Journal: The Bacteriophages (The Viruses) / Year: 1988
Title: Biology of the Bacteriophage PhiX174
Authors: Hayashi, M. / Adyama, A. / Delwood, L. / Richardson, D.L. / Hayashi, M.N.
#5: Journal: Nature / Year: 1977
Title: Nucleoside Sequence of Bacteriophage PhiX174 DNA
Authors: Sanger, F. / Air, G.M. / Barrell, B.G. / Brown, N.L. / Coulson, A.R. / Fiddes, J.C. / Hutchinson, C.A. / Slocombe, P.M. / Smith, M.
History
DepositionDec 3, 1991Deposition site: BNL / Processing site: BNL
Revision 1.0Dec 3, 1991Provider: repository / Type: Initial release
Revision 1.1May 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*AP*AP*AP*AP*C)-3')
1: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
2: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
3: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)


Theoretical massNumber of molelcules
Total (without water)73,0904
Polymers73,0904
Non-polymers00
Water3,207178
1
A: DNA (5'-D(*AP*AP*AP*AP*C)-3')
1: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
2: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
3: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
x 60


Theoretical massNumber of molelcules
Total (without water)4,385,394240
Polymers4,385,394240
Non-polymers00
Water4,324240
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: DNA (5'-D(*AP*AP*AP*AP*C)-3')
1: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
2: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
3: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
x 5


  • icosahedral pentamer
  • 365 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)365,45020
Polymers365,45020
Non-polymers00
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: DNA (5'-D(*AP*AP*AP*AP*C)-3')
1: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
2: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
3: PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)
x 6


  • icosahedral 23 hexamer
  • 439 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)438,53924
Polymers438,53924
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)305.580, 360.780, 299.460
Angle α, β, γ (deg.)90.00, 92.89, 90.00
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: DNA chain DNA (5'-D(*AP*AP*AP*AP*C)-3')


Mass: 1497.052 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)


Mass: 48423.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Species (production host): Escherichia coli / Production host: Escherichia coli C (bacteria) / Strain (production host): C / References: UniProt: P03641
#3: Protein PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)


Mass: 19061.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Species (production host): Escherichia coli / Production host: Escherichia coli C (bacteria) / Strain (production host): C / References: UniProt: P03643
#4: Protein/peptide PROTEIN (SUBUNIT OF BACTERIOPHAGE PHIX174)


Mass: 4107.821 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage phiX174 (virus) / Genus: Microvirus / Species: Enterobacteria phage phiX174 sensu lato / Species (production host): Escherichia coli / Production host: Escherichia coli C (bacteria) / Strain (production host): C / References: UniProt: P69592
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE NUCLEIC ACID RESIDUES ARE LABELLED A AND C. WHILE THE PYRIMIDINE AND PURINE NATURES OF THE ...THE NUCLEIC ACID RESIDUES ARE LABELLED A AND C. WHILE THE PYRIMIDINE AND PURINE NATURES OF THE RESIDUES WERE APPARENT, THE SIDE CHAINS COULD NOT ACTUALLY BE DISTINGUISHED. RESIDUE A 0 REFERS TO THE O3' OF THE PREVIOUS NUCLEIC ACID. THE NUCLEOTIDE BASES ARE UNREFINED AT PRESENT, BEING OBSERVED ONLY IN A DIFFERENCE MAP BETWEEN DATA FROM 114S AND 70S PARTICLES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: referred to J.Mol.Biol. 212.345-350 1990
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
190-93 mMbis-Tris methane1reservoir
21.5-2.0 %(w/v)PEG80001reservoir
30.125 mg/mlvirus1drop
490-93 mMbis-Tris methane1drop
51.5-2.0 %(w/v)PEG80001drop

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 9999 Å / Num. obs: 1000304 / Rmerge(I) obs: 0.129
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.9 Å / % possible obs: 27 % / Num. unique obs: 92108

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 3→6 Å / Rfactor obs: 0.209 / σ(F): 5
Details: ALL 175 AMINO ACIDS OF GPG, ALL 426 AMINO ACIDS OF GPF AND ALL BUT THE FIRST AMINO ACID OF GPJ WERE BUILT. ALSO FOUR NUCLEOTIDES (A 0-4) WERE BUILT, ALTHOUGH THE CHOICE OF NUCLEOTIDE BASES WERE ARBITRARY.
Refinement stepCycle: LAST / Resolution: 3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5037 83 0 178 5298
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d3.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 6 Å / σ(F): 5 / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.1

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