+Open data
-Basic information
Entry | Database: PDB / ID: 6y5x | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of apo New Jersey Polyomavirus VP1 | ||||||
Components | VP1 | ||||||
Keywords | VIRAL PROTEIN / Major Capsid Protein / Polyomavirus | ||||||
Function / homology | Function and homology information | ||||||
Biological species | New Jersey polyomavirus-2013 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Stroh, L.J. / Rustmeier, N.H. / Stehle, T. | ||||||
Funding support | Germany, 1items
| ||||||
Citation | Journal: Mbio / Year: 2020 Title: Structural Basis and Evolution of Glycan Receptor Specificities within the Polyomavirus Family. Authors: Stroh, L.J. / Rustmeier, N.H. / Blaum, B.S. / Botsch, J. / Rossler, P. / Wedekink, F. / Lipkin, W.I. / Mishra, N. / Stehle, T. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6y5x.cif.gz | 548.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6y5x.ent.gz | 445 KB | Display | PDB format |
PDBx/mmJSON format | 6y5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/6y5x ftp://data.pdbj.org/pub/pdb/validation_reports/y5/6y5x | HTTPS FTP |
---|
-Related structure data
Related structure data | 6y5yC 6y5zC 6y60C 6y61C 6y63C 6y64C 6y65C 6y66C 6y67C 6y6aC 6y9iC 4fmgS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||
2 |
| ||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 34096.566 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) New Jersey polyomavirus-2013 / Gene: VP1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta 2 / References: UniProt: A0A024B5J2 #2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.35 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Succinic acid, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 93.15 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 1, 2014 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→48.31 Å / Num. obs: 143717 / % possible obs: 99.93 % / Redundancy: 5.78 % / Biso Wilson estimate: 24.66 Å2 / CC1/2: 0.983 / Rrim(I) all: 0.254 / Net I/σ(I): 6.66 |
Reflection shell | Resolution: 2.3→2.382 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 1.58 / Num. unique obs: 14225 / CC1/2: 0.645 / Rrim(I) all: 1.027 / % possible all: 99.96 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4FMG Resolution: 2.3→48.309 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.26
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→48.309 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|