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Yorodumi- PDB-4dyt: Crystal Structure of WSN/A Influenza Nucleoprotein with Three Mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dyt | ||||||
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Title | Crystal Structure of WSN/A Influenza Nucleoprotein with Three Mutations (E53D, Y289H, Y313V) | ||||||
Components | Nucleocapsid protein | ||||||
Keywords | VIRAL PROTEIN | ||||||
Function / homology | Function and homology information helical viral capsid / viral penetration into host nucleus / host cell / viral nucleocapsid / symbiont entry into host cell / ribonucleoprotein complex / 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: 3 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 | 4dyt.cif.gz | 232.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dyt.ent.gz | 177.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dyt_validation.pdf.gz | 446.5 KB | Display | wwPDB validaton report |
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Full document | 4dyt_full_validation.pdf.gz | 458.9 KB | Display | |
Data in XML | 4dyt_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 4dyt_validation.cif.gz | 59.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dy/4dyt ftp://data.pdbj.org/pub/pdb/validation_reports/dy/4dyt | HTTPS FTP |
-Related structure data
Related structure data | 4dyaC 4dybC 4dynC 4dypC 4dysC 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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Unit cell |
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-Components
#1: Protein | Mass: 56834.148 Da / Num. of mol.: 3 / Mutation: E53D,Y289H,Y313V 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: 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: 2.29 Å3/Da / Density % sol: 46.4 % |
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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: 3→45.08 Å / Num. all: 28852 / Num. obs: 28852 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→45.08 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.807 / WRfactor Rfree: 0.337 / WRfactor Rwork: 0.2728 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7214 / SU B: 30.175 / SU ML: 0.56 / SU Rfree: 0.5909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.591 / 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: 124.24 Å2 / Biso mean: 82.4367 Å2 / Biso min: 15.88 Å2
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Refinement step | Cycle: LAST / Resolution: 3→45.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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