+
Open data
-
Basic information
| Entry | Database: PDB / ID: 4mbx | ||||||
|---|---|---|---|---|---|---|---|
| Title | Structure of unliganded B-Lymphotropic Polyomavirus VP1 | ||||||
Components | Major Capsid Protein VP1 | ||||||
Keywords | VIRAL PROTEIN / jelly roll / polyomavirus / viral capsid (structural) protein / DNA encapsidation / receptor binding / Sialylated oligosaccharides / Viral Coat Protein | ||||||
| Function / homology | Function and homology informationT=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity Similarity search - Function | ||||||
| Biological species | B-lymphotropic polyomavirus | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Khan, Z.M. / Neu, U. / Schuch, B. / Stehle, T. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013Title: 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 |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 4mbx.cif.gz | 1 MB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb4mbx.ent.gz | 898.2 KB | Display | PDB format |
| PDBx/mmJSON format | 4mbx.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4mbx_validation.pdf.gz | 520.2 KB | Display | wwPDB validaton report |
|---|---|---|---|---|
| Full document | 4mbx_full_validation.pdf.gz | 533.8 KB | Display | |
| Data in XML | 4mbx_validation.xml.gz | 113.8 KB | Display | |
| Data in CIF | 4mbx_validation.cif.gz | 160.6 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mb/4mbx ftp://data.pdbj.org/pub/pdb/validation_reports/mb/4mbx | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4mbyC ![]() 4mbzC ![]() 1vpnS C: citing same article ( S: Starting model for refinement |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||
| 2 | ![]()
| ||||||||||||||||||||||||||||||||||||||||||||
| Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||
| Noncrystallographic symmetry (NCS) | NCS oper:
|
-
Components
| #1: Protein | Mass: 30125.059 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) B-lymphotropic polyomavirus / Gene: VP1 / Plasmid: pET15b / Production host: ![]() #2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.31 % |
|---|---|
| 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 |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å |
| Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2012 |
| Radiation | Monochromator: Si(111) channel cut / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
| Reflection | Resolution: 1.92→40 Å / Num. all: 249079 / Num. obs: 246146 / % possible obs: 98.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.97 % / Net I/σ(I): 10.5 |
| Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 3.05 % / Mean I/σ(I) obs: 1.67 / % possible all: 99.5 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: PDB ENTRY 1VPN Resolution: 1.92→39.38 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.822 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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: 29.373 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.92→39.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




B-lymphotropic polyomavirus
X-RAY DIFFRACTION
Citation












PDBj









