+Open data
-Basic information
Entry | Database: PDB / ID: 5j96 | ||||||
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Title | Crystal structure of Slow Bee Paralysis Virus at 3.4A resolution | ||||||
Components |
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Keywords | VIRUS / icosahedral virus / honeybee / protrusion | ||||||
Function / homology | Function and homology information host cell membrane / viral capsid / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding ...host cell membrane / viral capsid / RNA helicase activity / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Slow bee paralysis virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.41 Å | ||||||
Authors | Kalynych, S. / Levdansky, Y. / Palkova, L. / Plevka, P. | ||||||
Citation | Journal: J.Virol. / Year: 2016 Title: Virion Structure of Iflavirus Slow Bee Paralysis Virus at 2.6-Angstrom Resolution. Authors: Kalynych, S. / Pridal, A. / Palkova, L. / Levdansky, Y. / de Miranda, J.R. / Plevka, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j96.cif.gz | 187.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j96.ent.gz | 147 KB | Display | PDB format |
PDBx/mmJSON format | 5j96.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/5j96 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/5j96 | HTTPS FTP |
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-Related structure data
Related structure data | 5cdcC 5cddC 5j98C 3napS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 30307.211 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Slow bee paralysis virus / Details (production host): pupae / Production host: Apis mellifera (honey bee) / References: UniProt: A7LM73 |
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#2: Protein | Mass: 29824.205 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Slow bee paralysis virus / Details (production host): pupae / Production host: Apis mellifera (honey bee) / References: UniProt: A7LM73 |
#3: Protein | Mass: 47623.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Slow bee paralysis virus / Details (production host): pupae / Production host: Apis mellifera (honey bee) / References: UniProt: A7LM73 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Description: small cubes with 30-50 micrometer long edges |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: NaCitrate pH 6.5, 5% (v/v) PEG-4,000, 0.2M NDSB-2 / Temp details: room temperature |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.994 Å |
Detector | Type: DECTRIS PILATUS3 X 1M / Detector: PIXEL / Date: Oct 1, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.994 Å / Relative weight: 1 |
Reflection | Resolution: 3.41→70.7 Å / Num. obs: 92015 / % possible obs: 87.4 % / Redundancy: 6 % / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3.41→3.45 Å / Rmerge(I) obs: 1.26 / Mean I/σ(I) obs: 0.4 / % possible all: 43.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NAP Resolution: 3.41→70.7 Å / Cross valid method: NONE
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Refinement step | Cycle: LAST / Resolution: 3.41→70.7 Å
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