[English] 日本語
Yorodumi- PDB-6ln0: Crystal structure of three main domains of nonstructural protein ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ln0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of three main domains of nonstructural protein 3 from Coronavirus | |||||||||
Components | Non-structural protein 3 | |||||||||
Keywords | VIRAL PROTEIN / nonstructural protein 3 | |||||||||
Function / homology | Function and homology information RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / methylation / endonuclease activity / DNA helicase ...RNA exonuclease activity / endoplasmic reticulum-Golgi intermediate compartment / host cell membrane / DNA helicase activity / methyltransferase activity / host cell endoplasmic reticulum-Golgi intermediate compartment / omega peptidase activity / methylation / endonuclease activity / DNA helicase / membrane => GO:0016020 / RNA helicase activity / host cell perinuclear region of cytoplasm / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding / zinc ion binding / ATP binding Similarity search - Function | |||||||||
Biological species | Porcine deltacoronavirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.455 Å | |||||||||
Authors | Li, M.X. / Peng, G.Q. | |||||||||
Citation | Journal: Emerg Microbes Infect / Year: 2021 Title: Structure of the multiple functional domains from coronavirus nonstructural protein 3. Authors: Li, M. / Ye, G. / Si, Y. / Shen, Z. / Liu, Z. / Shi, Y. / Xiao, S. / Fu, Z.F. / Peng, G. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ln0.cif.gz | 97.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ln0.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 6ln0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ln0_validation.pdf.gz | 789 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6ln0_full_validation.pdf.gz | 795.4 KB | Display | |
Data in XML | 6ln0_validation.xml.gz | 17.3 KB | Display | |
Data in CIF | 6ln0_validation.cif.gz | 23 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ln/6ln0 ftp://data.pdbj.org/pub/pdb/validation_reports/ln/6ln0 | HTTPS FTP |
-Related structure data
Related structure data | 3ewoS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 49701.176 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Porcine deltacoronavirus / Gene: ORF1ab / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A222YV61 |
---|---|
#2: Chemical | ChemComp-ZN / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.44 Å3/Da / Density % sol: 64.29 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, imidazole, Bis-tris |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.978 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.45→50 Å / Num. obs: 22938 / % possible obs: 98.8 % / Redundancy: 16.2 % / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.035 / Rrim(I) all: 0.145 / Χ2: 2.416 / Net I/σ(I): 8 / Num. measured all: 372635 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ewo Resolution: 2.455→39.018 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 29.4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 106.57 Å2 / Biso mean: 60.0475 Å2 / Biso min: 29.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.455→39.018 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|