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Yorodumi- PDB-2bpa: ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bpa | ||||||
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Title | ATOMIC STRUCTURE OF SINGLE-STRANDED DNA BACTERIOPHAGE PHIX174 AND ITS FUNCTIONAL IMPLICATIONS | ||||||
Components |
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Keywords | Virus/DNA / PROTEIN-DNA COMPLEX / SINGLE STRAND / Icosahedral virus / Virus-DNA COMPLEX | ||||||
Function / homology | Function and homology information modulation by virus 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 | ||||||
Biological species | Enterobacteria phage phiX174 (virus) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | ||||||
Authors | McKenna, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bpa.cif.gz | 144.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bpa.ent.gz | 111.2 KB | Display | PDB format |
PDBx/mmJSON format | 2bpa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bpa ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bpa | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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5 |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: DNA chain | Mass: 1497.052 Da / Num. of mol.: 1 / Source method: obtained synthetically |
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#2: Protein | 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 | 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 | 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 / |
Sequence details | THE 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 |
-Experimental details
-Experiment
Experiment | Method: 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 | ||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative 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 |
-Processing
Software | Name: PROLSQ / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 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 step | Cycle: LAST / Resolution: 3→6 Å
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Refine LS restraints |
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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
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