+Open data
-Basic information
Entry | Database: PDB / ID: 1gav | ||||||
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Title | BACTERIOPHAGE GA PROTEIN CAPSID | ||||||
Components | BACTERIOPHAGE GA PROTEIN CAPSID | ||||||
Keywords | VIRUS / BACTERIOPHAGE / CAPSID / COAT PROTEIN / 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 GA (virus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Tars, K. / Bundule, M. / Liljas, L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1997 Title: The crystal structure of bacteriophage GA and a comparison of bacteriophages belonging to the major groups of Escherichia coli leviviruses. Authors: Tars, K. / Bundule, M. / Fridborg, K. / Liljas, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gav.cif.gz | 1015.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gav.ent.gz | 861 KB | Display | PDB format |
PDBx/mmJSON format | 1gav.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ga/1gav ftp://data.pdbj.org/pub/pdb/validation_reports/ga/1gav | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 13635.385 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage GA (virus) / Genus: LevivirusEmesvirus / Species: Enterobacteria phage BZ13 / References: UniProt: P07234 |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 5.53 Å3/Da / Density % sol: 77.77 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 280 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 24, 1995 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 126364 / % possible obs: 68 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 3.4→3.58 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 1.8 / % possible all: 56 |
Reflection shell | *PLUS % possible obs: 56 % / Num. unique obs: 15134 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→30 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
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Displacement parameters | Biso mean: 18 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→3.46 Å / Total num. of bins used: 20 /
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Rfactor obs: 0.241 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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