[English] 日本語
![](img/lk-miru.gif)
- PDB-7b6v: Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pent... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7b6v | ||||||
---|---|---|---|---|---|---|---|
Title | Sheep Polyomavirus VP1 in complex with 5 mM Forssman antigen pentaose and 20 mM 3'-sialyllactosamine | ||||||
![]() | Capsid protein VP1 | ||||||
![]() | VIRAL PROTEIN / polyomavirus / capsid protein / VP1 / glycan complex | ||||||
Function / homology | ![]() T=7 icosahedral viral capsid / virion attachment to host cell / structural molecule activity / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rustmeier, N.H. / Stehle, T. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: A novel and highly specific Forssman antigen-binding protein from sheep polyomavirus Authors: Rustmeier, N.H. / Silva, L.M. / Di Maio, A. / Mueller, J.C. / Herrmann, A. / Feizi, T. / Liu, Y. / Stehle, T. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 585.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 7b6sC ![]() 7b6tC ![]() 7b6uC ![]() 6y61S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 10 molecules AAABBBCCCDDDEEEFFFGGGHHHIIIJJJ
#1: Protein | Mass: 30577.434 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
---|
-Sugars , 3 types, 15 molecules ![](data/chem/img/SIA.gif)
#2: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | 2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)- ...2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose-(1-4)-beta-D-glucopyranose | Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #4: Sugar | ChemComp-SIA / |
---|
-Non-polymers , 5 types, 2367 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-MG / #6: Chemical | #7: Chemical | ChemComp-PGE / | #8: Chemical | ChemComp-PEG / | #9: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.37 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: KSCN, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N | ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 19, 2019 | ||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength | Wavelength: 1.00004 Å / Relative weight: 1 | ||||||||||||||||||
Reflection twin |
| ||||||||||||||||||
Reflection | Resolution: 1.798→48.85 Å / Num. obs: 390469 / % possible obs: 99.8 % / Redundancy: 9.9 % / Biso Wilson estimate: 28.5 Å2 / CC1/2: 0.997 / Rrim(I) all: 0.162 / Net I/σ(I): 11.02 | ||||||||||||||||||
Reflection shell | Resolution: 1.8→1.91 Å / Mean I/σ(I) obs: 1.51 / Num. unique obs: 62546 / CC1/2: 0.471 / Rrim(I) all: 1.273 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6Y61 Resolution: 1.798→48.846 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.168 / WRfactor Rwork: 0.146 / Average fsc free: 0.9726 / Average fsc work: 0.9809 / Cross valid method: FREE R-VALUE / ESU R: 0.017 / ESU R Free: 0.017 Details: Hydrogens have been added in their riding positions
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.646 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.798→48.846 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|