[English] 日本語
Yorodumi- PDB-6x0r: A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H -
+Open data
-Basic information
Entry | Database: PDB / ID: 6x0r | ||||||
---|---|---|---|---|---|---|---|
Title | A Circular Permutant of the Tobacco Mosaic Virus (TMV) mutant Q101H | ||||||
Components | Capsid protein Circular Permutant | ||||||
Keywords | VIRAL PROTEIN / Viral capsid proteins / self-assembling proteins / double-disk assembly | ||||||
Function / homology | Tobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / identical protein binding / Capsid protein Function and homology information | ||||||
Biological species | Tobacco mosaic virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Dai, J. / Knott, G.J. / Francis, M.B. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acs Nano / Year: 2021 Title: Protein-Embedded Metalloporphyrin Arrays Templated by Circularly Permuted Tobacco Mosaic Virus Coat Proteins. Authors: Dai, J. / Knott, G.J. / Fu, W. / Lin, T.W. / Furst, A.L. / Britt, R.D. / Francis, M.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6x0r.cif.gz | 1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6x0r.ent.gz | 788 KB | Display | PDB format |
PDBx/mmJSON format | 6x0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6x0r_validation.pdf.gz | 543.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6x0r_full_validation.pdf.gz | 556.7 KB | Display | |
Data in XML | 6x0r_validation.xml.gz | 74.9 KB | Display | |
Data in CIF | 6x0r_validation.cif.gz | 94.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/6x0r ftp://data.pdbj.org/pub/pdb/validation_reports/x0/6x0r | HTTPS FTP |
-Related structure data
Related structure data | 6x0qC 3kmlS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 13 - 152 / Label seq-ID: 13 - 152
|
-Components
#1: Protein | Mass: 17714.609 Da / Num. of mol.: 17 / Mutation: Q101H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tobacco mosaic virus (strain vulgare) / Strain: vulgare / Gene: CP / Production host: Escherichia coli (E. coli) / References: UniProt: P69687 |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.23 Å3/Da / Density % sol: 61.97 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M SPG buffer (0.0125 M succinic acid, 0.0438 M sodium phosphate, 0.0437 M glycine), 12%-18% (v/v) PEG 1500, pH 5.0-5.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1158 Å / Relative weight: 1 |
Reflection | Resolution: 2.81→136.52 Å / Num. obs: 91158 / % possible obs: 98 % / Redundancy: 6.9 % / Biso Wilson estimate: 69.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.81→2.86 Å / Redundancy: 6 % / Num. unique obs: 4016 / CC1/2: 0.651 / % possible all: 88.2 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3kml Resolution: 3→48.97 Å / SU ML: 0.3313 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.3397 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 126.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→48.97 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|