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Yorodumi- PDB-1fr5: PHAGE FR CAPSIDS WITH A FOUR RESIDUE DELETION IN THE COAT PROTEIN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fr5 | |||||||||
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Title | PHAGE FR CAPSIDS WITH A FOUR RESIDUE DELETION IN THE COAT PROTEIN FG LOOP | |||||||||
Components | BACTERIOPHAGE FR CAPSID | |||||||||
Keywords | VIRUS / VIRAL COAT PROTEIN / CAPSID / Icosahedral virus | |||||||||
Function / homology | Function and homology information T=3 icosahedral viral capsid / regulation of translation / structural molecule activity / RNA binding Similarity search - Function | |||||||||
Biological species | Enterobacteria phage fr (virus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Axblom, C. / Tars, K. / Fridborg, K. / Bundule, M. / Orna, L. / Liljas, L. | |||||||||
Citation | Journal: Virology / Year: 1998 Title: Structure of phage fr capsids with a deletion in the FG loop: implications for viral assembly. Authors: Axblom, C. / Tars, K. / Fridborg, K. / Orna, L. / Bundule, M. / Liljas, L. #1: Journal: J.Mol.Biol. / Year: 1994 Title: Crystal Structure of Bacteriophage Fr Capsids at 3.5 A Resolution Authors: Liljas, L. / Fridborg, K. / Valegard, K. / Bundule, M. / Pumpens, P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fr5.cif.gz | 75.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fr5.ent.gz | 60.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fr5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1fr5 ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1fr5 | HTTPS FTP |
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-Related structure data
Related structure data | 1frsS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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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: 13333.982 Da / Num. of mol.: 3 / Mutation: DEL(70-73) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage fr (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage MS2Bacteriophage MS2 / Plasmid: PFRS5 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P03614 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→20 Å / Num. obs: 52800 / % possible obs: 48 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.139 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 3.5→3.56 Å / Rmerge(I) obs: 0.387 / % possible all: 26 |
Reflection shell | *PLUS % possible obs: 26 % / Num. unique obs: 1419 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FRS Resolution: 3.5→30 Å / Isotropic thermal model: RESTRAINED
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Refinement step | Cycle: LAST / Resolution: 3.5→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.5→3.56 Å / Total num. of bins used: 20
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1F / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.351 |