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Yorodumi- PDB-1rb8: The phiX174 DNA binding protein J in two different capsid environ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rb8 | |||||||||
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Title | The phiX174 DNA binding protein J in two different capsid environments. | |||||||||
Components |
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Keywords | Virus/DNA / bacteriophage alpha3 / bacteriophage phiX174 / bacteriophage alpha3 chimera / alpha3 / phiX174 / three-dimentional structure / virion / Microviridae / 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 / structural molecule activity / virion attachment to host cell / DNA binding Similarity search - Function | |||||||||
Biological species | Enterobacteria phage phiX174 (virus) Enterobacteria phage alpha3 (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Bernal, R.A. / Hafenstein, S. / Esmeralda, R. / Fane, B.A. / Rossmann, M.G. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2004 Title: The phiX174 Protein J Mediates DNA Packaging and Viral Attachment to Host Cells. Authors: Bernal, R.A. / Hafenstein, S. / Esmeralda, R. / Fane, B.A. / Rossmann, M.G. #1: Journal: J.Mol.Biol. / Year: 2003 Title: Structural Studies of Bacteriophage Alpha3 Assembly Authors: Bernal, R.A. / Hafenstein, S. / Olson, N.H. / Bowman, V.D. / Chipman, P.R. / Baker, T.S. / Fane, B.A. / Rossmann, M.G. #2: Journal: J.Mol.Biol. / Year: 1999 Title: The role of scaffolding proteins in the assembly of the small, single-stranded DNA virus phiX174. Authors: Dokland, T. / Bernal, R.A. / Burch, A. / Pletnev, S. / Fane, B.A. / Rossmann, M.G. #3: 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. | |||||||||
History |
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Remark 400 | COMPOUND THE VIRUS IS A CHIMERA. THE CAPSID PROTEIN F AND THE SPIKE PROTEIN G ARE FROM ALPHA3 BUT ...COMPOUND THE VIRUS IS A CHIMERA. THE CAPSID PROTEIN F AND THE SPIKE PROTEIN G ARE FROM ALPHA3 BUT THE J PROTEIN WAS REPLACED BY THE J PROTEIN OF PHIX174. | |||||||||
Remark 999 | SEQUENCE RESIDUE 160 OF THE F PROTEIN IS AN ARG ACCORDING TO THE REPORTED SEQUENCE BUT NO DENSITY ...SEQUENCE RESIDUE 160 OF THE F PROTEIN IS AN ARG ACCORDING TO THE REPORTED SEQUENCE BUT NO DENSITY IS SEEN FOR THE SIDE CHAIN IN THE CRYSTAL STRUCTURE FOR THIS RESIDUE. AFTER A STRUCTURAL SEQUENCE ALIGNMENT WITH HOMOLOGOUS BACTERIOPHAGES PHIX174 AND G4, RESIDUE 160 WAS FOUND TO BE A GLYCINE IN THE OTHER PHAGES. CONSEQUENTLY, THE AUTHORS STATE RESIDUE 160 SHOULD BE A GLYCINE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rb8.cif.gz | 141.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rb8.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rb8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rb/1rb8 ftp://data.pdbj.org/pub/pdb/validation_reports/rb/1rb8 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 49294.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: wt alpha3 capsid protein F / Source: (natural) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / References: UniProt: P08767 |
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#2: Protein | Mass: 19598.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: wt alpha3 spike protein G / Source: (natural) Enterobacteria phage alpha3 (virus) / Genus: Microvirus / References: UniProt: P31281 |
#3: 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 / Gene: J / Production host: Escherichia coli (E. coli) / Strain (production host): recA- cells / References: UniProt: P69592 |
#4: DNA chain | Mass: 1183.845 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#5: Chemical | ChemComp-DC / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 4-7% PEG 8000, 100 mM sodium citrate pH 5.0, 40% glycerol, 0.02% sodium azide, 0.1% beta-mercapto-ethanol, 0.9M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→500 Å / Num. all: 342669 / Num. obs: 269234 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Biso Wilson estimate: 1 Å2 / Rmerge(I) obs: 0.097 |
Reflection shell | Resolution: 3.5→3.66 Å / Rmerge(I) obs: 0.157 / % possible all: 94.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Bacteriophage alpha3 wild-type structure Resolution: 3.5→92.91 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 112625.55 / Data cutoff high rms absF: 112625.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: the O3*-P bond between residue (X A 3 ) and Residue (X A 4 ) is 1.91A. The density for the nucleic acid in this region is very weak and therefore difficult to interpret.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.312307 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.5→92.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | |||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.66 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 8
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Xplor file |
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