+Open data
-Basic information
Entry | Database: PDB / ID: 4z5v | ||||||
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Title | Crystal Structure of MHV ns2 PDE Domain | ||||||
Components | Non-structural protein 2a | ||||||
Keywords | VIRAL PROTEIN / Murine hepatitis virus / ns2 protein / Phosphodiesterase | ||||||
Function / homology | Coronavirus NS2A / NS2A-like / Coronavirus NS2A protein / host cell cytoplasm / Non-structural protein 2a Function and homology information | ||||||
Biological species | Murine coronavirus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.049 Å | ||||||
Authors | Sui, B.K. / Huang, J.H. / Peng, G.Q. / Zhao, L. | ||||||
Citation | Journal: J.Gen.Virol. / Year: 2016 Title: Crystal structure of the mouse hepatitis virus ns2 phosphodiesterase domain that antagonizes RNase L activation Authors: Sui, B.K. / Huang, J.H. / Jha, B.K. / Yin, P. / Zhou, M. / Fu, Z.F. / Silverman, R.H. / Weiss, S.R. / Peng, G.Q. / Zhao, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z5v.cif.gz | 72.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z5v.ent.gz | 57.9 KB | Display | PDB format |
PDBx/mmJSON format | 4z5v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/4z5v ftp://data.pdbj.org/pub/pdb/validation_reports/z5/4z5v | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24139.852 Da / Num. of mol.: 2 / Fragment: UNP residues 2-199 Source method: isolated from a genetically manipulated source Details: phosphodiesterase / Source: (gene. exp.) Murine coronavirus (strain A59) / Strain: A59 / Gene: 2a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: P19738 |
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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: 4.4 Å3/Da / Density % sol: 72.9 % Description: the entry contains Friedel pairs in F_Plus/Minus columns |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 16% PEG3350, 0.1M succinic acid |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97907 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 14, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97907 Å / Relative weight: 1 |
Reflection | Resolution: 3.05→50 Å / Num. all: 32650 / Num. obs: 31292 / % possible obs: 99.9 % / Redundancy: 8.6 % / Biso Wilson estimate: 92.19 Å2 / Rpim(I) all: 0.023 / Rrim(I) all: 0.089 / Χ2: 1.277 / Net I/av σ(I): 32.926 / Net I/σ(I): 20.6 / Num. measured all: 274550 |
Reflection shell | Resolution: 3.05→3.16 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1752 / CC1/2: 0.899 / Rpim(I) all: 0.223 / Rrim(I) all: 0.903 / Χ2: 1.312 / Rejects: 0 / % possible all: 96.3 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 3.049→48.489 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.76 / Stereochemistry target values: ML Details: the entry contains Friedel pairs in F_Plus/Minus columns
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.37 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.049→48.489 Å
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Refine LS restraints |
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LS refinement shell |
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