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- PDB-4mbz: Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4mbz | |||||||||
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Title | Structure of B-Lymphotropic Polyomavirus VP1 in complex with 3'-sialyllactosamine | |||||||||
![]() | Major Capsid Protein VP1 | |||||||||
![]() | VIRAL PROTEIN / jelly roll / Polyomavirus / viral capsid (structural) protein / DNA encapsidation / receptor binding / Sialylated oligosaccharides | |||||||||
Function / homology | ![]() T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Khan, Z.M. / Neu, U. / Stehle, T. | |||||||||
![]() | ![]() Title: Structures of B-Lymphotropic Polyomavirus VP1 in Complex with Oligosaccharide Ligands. Authors: Neu, U. / Khan, Z.M. / Schuch, B. / Palma, A.S. / Liu, Y. / Pawlita, M. / Feizi, T. / Stehle, T. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.1 MB | Display | ![]() |
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PDB format | ![]() | 930.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
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Full document | ![]() | 2.8 MB | Display | |
Data in XML | ![]() | 126.6 KB | Display | |
Data in CIF | ![]() | 186.9 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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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 10 molecules ABCDEFGHIJ
#1: Protein | Mass: 30125.059 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 2 types, 7 molecules
#2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source #3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / 3'-sialyl-N-acetyllactosamine | |
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-Non-polymers , 5 types, 2953 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/IPA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-IPA / #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.41 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8 Details: 12% (v/v) Isopropanol, 0.2 M calcium chloride, 0.1 M sodium acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 13, 2012 |
Radiation | Monochromator: DCCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→50 Å / Num. all: 336648 / Num. obs: 333435 / % possible obs: 99.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Biso Wilson estimate: 27.3 Å2 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 24809 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: LPyV Native structure Resolution: 1.75→48.75 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.533 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.229 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→48.75 Å
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