[English] 日本語
Yorodumi- PDB-7ytu: Crystal structure of vaccinia virus G3/L5 sub-complex (SeMet-labe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ytu | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of vaccinia virus G3/L5 sub-complex (SeMet-labeled, P31 space group) | ||||||
Components |
| ||||||
Keywords | VIRAL PROTEIN / the components of entry-fusion complex | ||||||
Function / homology | Function and homology information symbiont entry into host cell / fusion of virus membrane with host plasma membrane / viral envelope / virion membrane / membrane Similarity search - Function | ||||||
Biological species | Vaccinia virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.504 Å | ||||||
Authors | Lin, S. / Yue, D. / Lu, G.W. | ||||||
Funding support | 1items
| ||||||
Citation | Journal: Emerg Microbes Infect / Year: 2023 Title: Crystal structure of vaccinia virus G3/L5 sub-complex reveals a novel fold with extended inter-molecule interactions conserved among orthopoxviruses. Authors: Lin, S. / Yue, D. / Yang, F. / Chen, Z. / He, B. / Cao, Y. / Dong, H. / Li, J. / Zhao, Q. / Lu, G. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7ytu.cif.gz | 66.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7ytu.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 7ytu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yt/7ytu ftp://data.pdbj.org/pub/pdb/validation_reports/yt/7ytu | HTTPS FTP |
---|
-Related structure data
Related structure data | 7yttC C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 10546.639 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Western Reserve) Strain: Western Reserve / Gene: VACWR079, G3L / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68458 |
---|---|
#2: Protein | Mass: 9221.222 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus (strain Western Reserve) Strain: Western Reserve / Gene: VACWR092, L5R / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P68623 |
#3: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.85 Å3/Da / Density % sol: 33.48 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Sodium formate (pH 7.0), 12% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 5, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97892 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 22077 / % possible obs: 99.6 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 19.46 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.43 / Num. unique obs: 2153 / % possible all: 96.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 1.504→31.56 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 25.59 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.504→31.56 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -3.0903 Å / Origin y: -14.4565 Å / Origin z: 1.309 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |