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- PDB-7dda: Envelope protein VP37 a crystal structure from White Spot Syndrom... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7dda | ||||||
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Title | Envelope protein VP37 a crystal structure from White Spot Syndrome Virus | ||||||
![]() | Envelope protein | ||||||
![]() | VIRAL PROTEIN / Envelope protein / Sulfate binding site / VP281 / VP37 / White spot syndrome virus (WSSV) | ||||||
Function / homology | viral envelope / Envelope protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Somsoros, W. / Sangawa, T. / Takebe, K. / Attarataya, J. / Suzuki, M. / Khunrae, P. | ||||||
![]() | ![]() Title: Crystal structure of the C-terminal domain of envelope protein VP37 from white spot syndrome virus reveals sulphate binding sites responsible for heparin binding. Authors: Somsoros, W. / Sangawa, T. / Takebe, K. / Attarataya, J. / Wongprasert, K. / Senapin, S. / Rattanarojpong, T. / Suzuki, M. / Khunrae, 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 | ![]() | 41.5 KB | Display | ![]() |
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PDB format | ![]() | 25.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 926.9 KB | Display | ![]() |
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Full document | ![]() | 927.1 KB | Display | |
Data in XML | ![]() | 6.8 KB | Display | |
Data in CIF | ![]() | 8.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18984.098 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Details (production host): pET15bThio, a pET15b (+) from Novagen which was modified to have thioredoxin and TEV cleavage site encoding sequence inserted upstream of the multiple cloning region Production host: ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.11 % / Description: Hexagonal shaped crystals |
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Crystal grow | Temperature: 293.2 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.5 M Ammonium sulfate, 100 mM Bis-Tris pH 6.5, 100 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 9, 2016 |
Radiation | Monochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.505→44.691 Å / Num. obs: 8198 / % possible obs: 96.2 % / Redundancy: 37.1 % / Biso Wilson estimate: 28.51 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.014 / Rrim(I) all: 0.086 / Net I/σ(I): 43.6 |
Reflection shell | Resolution: 2.505→2.548 Å / Redundancy: 36.1 % / Rmerge(I) obs: 0.327 / Mean I/σ(I) obs: 12.2 / Num. unique obs: 410 / CC1/2: 0.994 / CC star: 0.998 / Rpim(I) all: 0.054 / Rrim(I) all: 0.331 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.26 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.51→40.74 Å
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Refine LS restraints |
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LS refinement shell |
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