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Open data
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Basic information
Entry | Database: PDB / ID: 5j96 | ||||||
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Title | Crystal structure of Slow Bee Paralysis Virus at 3.4A resolution | ||||||
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![]() | VIRUS / icosahedral virus / honeybee / protrusion | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kalynych, S. / Levdansky, Y. / Palkova, L. / Plevka, P. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.2 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 451.9 KB | Display | ![]() |
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Full document | ![]() | 470.5 KB | Display | |
Data in XML | ![]() | 33.1 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5cdcC ![]() 5cddC ![]() 5j98C ![]() 3napS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() ![]() |
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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.) ![]() ![]() ![]() |
#3: Protein | Mass: 47623.910 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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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