+Open data
-Basic information
Entry | Database: PDB / ID: 5epw | ||||||
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Title | C-Terminal Domain Of Human Coronavirus Nl63 Nucleocapsid Protein | ||||||
Components | Nucleoprotein | ||||||
Keywords | VIRAL PROTEIN / NL63 coronavirus / N-protein / C-Terminal Domain | ||||||
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: 1.5 Å | ||||||
Authors | Szelazek, B. / Kabala, W. / Kus, K. / Zdzalik, M. / Golik, P. / Florek, D. / Burmistrz, M. / Pyrc, K. / Dubin, G. | ||||||
Funding support | Poland, 1items
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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 | 5epw.cif.gz | 62.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5epw.ent.gz | 44.4 KB | Display | PDB format |
PDBx/mmJSON format | 5epw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/5epw ftp://data.pdbj.org/pub/pdb/validation_reports/ep/5epw | HTTPS FTP |
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-Related 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: 14775.406 Da / Num. of mol.: 2 / Fragment: CTD, UNP residues 221-340 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: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.62 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M PCTP pH 8.0, 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 0.918409 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 26, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.918409 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→49.83 Å / Num. all: 399891 / Num. obs: 39167 / % possible obs: 100 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 9.7 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→49.83 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.337 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.069 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.307 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→49.83 Å
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