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Yorodumi- PDB-4lmt: Structure of The N-terminal domain of Coronavirus Nucleocapsid Pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lmt | ||||||
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Title | Structure of The N-terminal domain of Coronavirus Nucleocapsid Protein complexed with NSC663284 | ||||||
Components | Nucleoprotein | ||||||
Keywords | RNA BINDING PROTEIN / HCoV-OC43 / Nucleocapsid prtoein / N-termainl domain / RNA binding | ||||||
Function / homology | Function and homology information host cell endoplasmic reticulum-Golgi intermediate compartment / host cell Golgi apparatus / viral nucleocapsid / ribonucleoprotein complex / RNA binding Similarity search - Function | ||||||
Biological species | Human coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Lin, S.Y. / Liu, C.L. / Hou, M.H. | ||||||
Citation | Journal: To be Published Title: Domain of Coronavirus Nucleocapsid Protein complexed with NSC663284 Authors: Lin, S.Y. / Liu, C.L. / Hou, M.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lmt.cif.gz | 43.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lmt.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 4lmt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lmt_validation.pdf.gz | 733.8 KB | Display | wwPDB validaton report |
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Full document | 4lmt_full_validation.pdf.gz | 739 KB | Display | |
Data in XML | 4lmt_validation.xml.gz | 9.6 KB | Display | |
Data in CIF | 4lmt_validation.cif.gz | 12.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/4lmt ftp://data.pdbj.org/pub/pdb/validation_reports/lm/4lmt | HTTPS FTP |
-Related structure data
Related structure data | 4j3kS S: Starting model for refinement |
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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: 15437.901 Da / Num. of mol.: 1 / Fragment: UNP residues 55-188 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human coronavirus / Strain: OC43 / Gene: N / Production host: Escherichia coli (E. coli) / References: UniProt: Q6SA23, UniProt: P33469*PLUS |
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#2: Chemical | ChemComp-CQD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG1500, 0.25M SPG, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: LN2-Cooled, Fixed-Exit Double Crystal Monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.71→30 Å / Num. all: 17432 / Num. obs: 17432 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 13.13 Å2 |
Reflection shell | Resolution: 1.71→1.77 Å / % possible all: 100 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4J3K Resolution: 1.71→22.732 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7818 / SU ML: 0.21 / σ(F): 1.34 / Phase error: 28.56 / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.92 Å2 / Biso mean: 20.3821 Å2 / Biso min: 2.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.71→22.732 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12
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