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Yorodumi- PDB-4dyp: Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-83178... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dyp | ||||||
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Title | Crystal Structure of WSN/A Influenza Nucleoprotein with BMS-831780 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: 2.82 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dyp.cif.gz | 165.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dyp.ent.gz | 124.7 KB | Display | PDB format |
PDBx/mmJSON format | 4dyp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dyp_validation.pdf.gz | 959.9 KB | Display | wwPDB validaton report |
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Full document | 4dyp_full_validation.pdf.gz | 964.5 KB | Display | |
Data in XML | 4dyp_validation.xml.gz | 29.2 KB | Display | |
Data in CIF | 4dyp_validation.cif.gz | 40 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dyp ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dyp | HTTPS FTP |
-Related structure data
Related structure data | 4dyaC 4dybC 4dynC 4dysC 4dytC 5iboC 6dqcC 6dqdC 6dqeC 6dqfC 7rt0C 7ugbC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.72 % |
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: 2.82→103.627 Å / Num. obs: 25480 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 61.346 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 24.01 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.82→48.85 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.2776 / WRfactor Rwork: 0.2457 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7652 / SU B: 16.339 / SU ML: 0.324 / SU R Cruickshank DPI: 2.6956 / SU Rfree: 0.4185 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.696 / ESU R Free: 0.419 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 91.32 Å2 / Biso mean: 53.8592 Å2 / Biso min: 21.78 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.82→48.85 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.82→2.895 Å / Total num. of bins used: 20
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