[English] 日本語
Yorodumi- PDB-4dya: Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-88598... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dya | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-885986 Ligand Bound | ||||||
Components | Nucleocapsid protein | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Function and homology information helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / ribonucleoprotein complex / symbiont entry into host cell / host cell nucleus / structural molecule activity / RNA binding / identical protein binding Similarity search - Function | ||||||
Biological species | Influenza A virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å | ||||||
Authors | Lewis, H.A. / Baldwin, E.T. / Steinbacher, S. / Maskos, K. / Mortl, M. / Kiefersauer, R. / Edavettal, S. / McDonnell, P.A. / Pearce, B.C. / Langley, D.R. | ||||||
Citation | Journal: To be Published Title: To be determined Authors: Lewis, H.A. / Baldwin, E.T. / Steinbacher, S. / Maskos, K. / Mortl, M. / Kiefersauer, R. / Edavettal, S. / McDonnell, P.A. / Pearce, B.C. / Langley, D.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4dya.cif.gz | 170.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4dya.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 4dya.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dya_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4dya_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4dya_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 4dya_validation.cif.gz | 40.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dya ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dya | HTTPS FTP |
-Related structure data
Related structure data | 4dybC 4dynC 4dypC 4dysC 4dytC 5iboC 6dqcC 6dqdC 6dqeC 6dqfC 7rt0C 7ugbC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 56806.047 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Influenza A virus / Strain: A/WSN/1933(H1N1) / Gene: NP / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / References: UniProt: B4URF1, UniProt: Q1K9H2*PLUS #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.55 % |
---|
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Detector | Type: PSI PILATUS 6M / Detector: PIXEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.75→102.881 Å / Num. obs: 26867 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 53.888 Å2 / Rmerge(I) obs: 0.103 / Net I/σ(I): 15.61 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→48.51 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.874 / WRfactor Rfree: 0.2517 / WRfactor Rwork: 0.2253 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7709 / SU B: 16.124 / SU ML: 0.325 / SU R Cruickshank DPI: 2.0911 / SU Rfree: 0.4094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.091 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 84.4 Å2 / Biso mean: 48.7115 Å2 / Biso min: 7.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.75→48.51 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.75→2.822 Å / Total num. of bins used: 20
|