+Open data
-Basic information
Entry | Database: PDB / ID: 6z4u | ||||||
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Title | X-ray Crystallographic Structure of Orf9b from SARS-CoV-2 | ||||||
Components | Protein 9b | ||||||
Keywords | VIRAL PROTEIN / orf9b | ||||||
Function / homology | Function and homology information 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 / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial membrane ...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 / protein sequestering activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / DDX58/IFIH1-mediated induction of interferon-alpha/beta / mitochondrial membrane / mitochondrial outer membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / virus-mediated perturbation of host defense response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / identical protein binding Similarity search - Function | ||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Weeks, S.D. / De Graef, S. / Munawar, A. | ||||||
Citation | Journal: To Be Published Title: X-ray Crystallographic Structure of Orf9b from SARS-CoV-2 Authors: Weeks, S.D. / De Graef, S. / Munawar, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6z4u.cif.gz | 81 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6z4u.ent.gz | 57.6 KB | Display | PDB format |
PDBx/mmJSON format | 6z4u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6z4u_validation.pdf.gz | 593 KB | Display | wwPDB validaton report |
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Full document | 6z4u_full_validation.pdf.gz | 593.2 KB | Display | |
Data in XML | 6z4u_validation.xml.gz | 8.8 KB | Display | |
Data in CIF | 6z4u_validation.cif.gz | 11.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z4/6z4u ftp://data.pdbj.org/pub/pdb/validation_reports/z4/6z4u | HTTPS FTP |
-Related structure data
Related structure data | 2cmeS 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: 10808.636 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Severe acute respiratory syndrome coronavirus 2 Production host: Escherichia coli (E. coli) / Variant (production host): T7 Express / References: UniProt: P0DTD2 #2: Chemical | ChemComp-15P / | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.83 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Protein at 8.3 mg/ml in 20 mM Tris pH 7.0 150 mM NaCl, 1mM DTT was mixed in a 3:2 ratio with the MORPHEUS crystallization screen condition E4 (Tube 2-4; 0.12 M Ethylene glycols 0.1 M Buffer ...Details: Protein at 8.3 mg/ml in 20 mM Tris pH 7.0 150 mM NaCl, 1mM DTT was mixed in a 3:2 ratio with the MORPHEUS crystallization screen condition E4 (Tube 2-4; 0.12 M Ethylene glycols 0.1 M Buffer System 1 pH 6.5 37.5 % v/v Precipitant Mix 4) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979329 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 15, 2020 | ||||||||||||||||||||||||
Radiation | Monochromator: Si 111 double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.979329 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.95→36.77 Å / Num. obs: 13064 / % possible obs: 99.3 % / Redundancy: 7.4 % / CC1/2: 0.934 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.05 / Rrim(I) all: 0.133 / Net I/σ(I): 8.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CME Resolution: 1.95→36.77 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / SU B: 9.017 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.54 Å2 / Biso mean: 33.585 Å2 / Biso min: 16.12 Å2
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Refinement step | Cycle: final / Resolution: 1.95→36.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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