+
Open data
-
Basic information
Entry | Database: PDB / ID: 9mzb | ||||||
---|---|---|---|---|---|---|---|
Title | X-ray crystallographic structure of Orf9b Apo Homodimer | ||||||
![]() | ORF9b protein | ||||||
![]() | VIRAL PROTEIN / Refolded / Apo-Homodimer / Type-1 Interferon Suppressor / Fold-switcher | ||||||
Function / homology | ![]() Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / negative regulation of mitochondrial fission / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta ...Translation of Accessory Proteins / outer mitochondrial membrane protein complex / negative regulation of defense response to virus / positive regulation of autophagosome assembly / negative regulation of mitochondrial fission / host cell mitochondrion / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / protein sequestering activity / mitochondrial membrane / DDX58/IFIH1-mediated induction of interferon-alpha/beta / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | San Felipe, C.J. / Fraser, J.S. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: X-ray Crystallographic Structure of Refolded Apo-Orf9b Homodimer Authors: San Felipe, C.J. / Fraser, J.S. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 109.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 80.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 10808.636 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: 9b / Production host: ![]() ![]() #2: Chemical | ChemComp-GLY / | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.04 Å3/Da / Density % sol: 59.47 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 1.2M Sodium Phosphate, 0.8M Potassium Phosphate, 0.2M Lithium Sulfate, and 0.1M Glycine pH 10.5 |
-Data collection
Diffraction | Mean temperature: 193.15 K / Ambient temp details: Cryogenic / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 21, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.116 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→37.64 Å / Num. obs: 12518 / % possible obs: 99.7 % / Redundancy: 4.9 % / Biso Wilson estimate: 97.42 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.06155 / Rpim(I) all: 0.03073 / Rrim(I) all: 0.06893 / Net I/σ(I): 11.49 |
Reflection shell | Resolution: 2.8→2.91 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.187 / Mean I/σ(I) obs: 0.93 / Num. unique obs: 1367 / CC1/2: 0.319 / CC star: 0.696 / Rpim(I) all: 0.7572 / Rrim(I) all: 1.414 / % possible all: 98.06 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 129.53 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→37.64 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 22.3149426092 Å / Origin y: -29.4025059655 Å / Origin z: -14.6729628711 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group | Selection details: all |