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Yorodumi- PDB-5n4k: N-terminal domain of a human Coronavirus NL63 nucleocapsid protein -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n4k | ||||||
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Title | N-terminal domain of a human Coronavirus NL63 nucleocapsid protein | ||||||
Components | Nucleoprotein | ||||||
Keywords | RNA BINDING PROTEIN / NUCLEOCAPSID PROTEIN | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / DNA binding / RNA binding Similarity search - Function | ||||||
Biological species | Human coronavirus NL63 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å | ||||||
Authors | Zdzalik, M. / Szelazek, B. / Kabala, W. / Golik, P. / Burmistrz, M. / Florek, D. / Kus, K. / Pyrc, K. / Dubin, G. | ||||||
Citation | Journal: J. Virol. / Year: 2017 Title: Structural Characterization of Human Coronavirus NL63 N Protein. Authors: Szelazek, B. / Kabala, W. / Kus, K. / Zdzalik, M. / Twarda-Clapa, A. / Golik, P. / Burmistrz, M. / Florek, D. / Wladyka, B. / Pyrc, K. / Dubin, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n4k.cif.gz | 79.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n4k.ent.gz | 59.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n4k_validation.pdf.gz | 458.5 KB | Display | wwPDB validaton report |
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Full document | 5n4k_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 5n4k_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 5n4k_validation.cif.gz | 26.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n4/5n4k ftp://data.pdbj.org/pub/pdb/validation_reports/n4/5n4k | HTTPS FTP |
-Related structure data
Related structure data | 5epwC 2bxxS S: Starting model for refinement 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: 17343.768 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus NL63 / Gene: N, 6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6Q1R8 #2: Chemical | ChemComp-SO4 / #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: 1.95 Å3/Da / Density % sol: 36.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: AMMONIUM SULPHATE, TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.49→50.61 Å / Num. obs: 42346 / % possible obs: 99.1 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 16.1 |
Reflection shell | Resolution: 1.49→1.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.095 / Mean I/σ(I) obs: 7.4 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2BXX Resolution: 1.49→41.65 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.112 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.077 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.82 Å2
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Refinement step | Cycle: LAST / Resolution: 1.49→41.65 Å
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Refine LS restraints |
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