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Open data
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Basic information
Entry | Database: PDB / ID: 5cdd | ||||||
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Title | Crystal Structure of Israel acute Paralysis Virus Pentamer | ||||||
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![]() | VIRUS / Pentamer / capsid / honeybee virus / pathogen | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Mullapudi, E. / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 151.4 KB | Display | ![]() |
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PDB format | ![]() | 118.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 409.9 KB | Display | ![]() |
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Full document | ![]() | 430 KB | Display | |
Data in XML | ![]() | 18.7 KB | Display | |
Data in CIF | ![]() | 26.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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3 | ![]()
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Unit cell |
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Symmetry | Point symmetry: (Schoenflies symbol: D5 (2x5 fold dihedral)) | ||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 23881.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 33353.836 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 22391.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M HEPES pH 7.5, 20% (w/v) PEG 10,000, 8% Ethylene glycol |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 9, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→70 Å / Num. obs: 240313 / % possible obs: 98.69 % / Redundancy: 4.2 % / Net I/σ(I): 2.67 |
-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Bsol: 20.0391 Å2 | ||||||||||||||||||||||||
Displacement parameters | Biso max: 104.08 Å2 / Biso mean: 42.0621 Å2 / Biso min: 7.21 Å2
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Refinement step | Cycle: final / Resolution: 2.7→70 Å
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Refine LS restraints |
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Xplor file |
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