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Yorodumi- PDB-7sf0: Crystal structure of Vaccinia Virus decapping enzyme D9 in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7sf0 | |||||||||
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Title | Crystal structure of Vaccinia Virus decapping enzyme D9 in complex with trinucleotide substrate | |||||||||
Components | DNA repair NTP-phosphohydrolase | |||||||||
Keywords | VIRAL PROTEIN / Nudix / decapping / mRNA cap | |||||||||
Function / homology | Viral protein D9 / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily / hydrolase activity / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / NTP-phosphohydrolase Function and homology information | |||||||||
Biological species | Vaccinia virus Western Reserve | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95000442951 Å | |||||||||
Authors | Peters, J.K. / Tibble, R.W. / Warminski, M. / Jemielity, J. / Gross, J.D. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Structure / Year: 2022 Title: Structure of the poxvirus decapping enzyme D9 reveals its mechanism of cap recognition and catalysis. Authors: Peters, J.K. / Tibble, R.W. / Warminski, M. / Jemielity, J. / Gross, J.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sf0.cif.gz | 76.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sf0.ent.gz | 44.3 KB | Display | PDB format |
PDBx/mmJSON format | 7sf0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sf0_validation.pdf.gz | 824.7 KB | Display | wwPDB validaton report |
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Full document | 7sf0_full_validation.pdf.gz | 826.3 KB | Display | |
Data in XML | 7sf0_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 7sf0_validation.cif.gz | 17.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/7sf0 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sf0 | HTTPS FTP |
-Related structure data
Related structure data | 7sezSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 26102.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vaccinia virus Western Reserve Gene: D9R, VACV_BRZ_SERRO2_112, VACV_CTGV_ALEH2_114, VACV_CTGV_CG04_114, VACV_CTGV_MI233-114, VACV_CTGV_VI04_114, VAC_IHDW1_116, VAC_TKT3_104, VAC_TKT4_104, VAC_TP3_119, VAC_TP5_119, VACV_CTGV_CM01_ ...Gene: D9R, VACV_BRZ_SERRO2_112, VACV_CTGV_ALEH2_114, VACV_CTGV_CG04_114, VACV_CTGV_MI233-114, VACV_CTGV_VI04_114, VAC_IHDW1_116, VAC_TKT3_104, VAC_TKT4_104, VAC_TP3_119, VAC_TP5_119, VACV_CTGV_CM01_114, VACV_TT10_141, VACV_TT11_141, VACV_TT12_141, VACV_TT8_141, VACV_TT9_141 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: L7QJE0 | ||||
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#2: Chemical | ChemComp-M7G / | ||||
#3: Chemical | ChemComp-NA / | ||||
#4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: sodium sulfate, PEG3350, Bis Tris propane pH 7.5, magnesium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.115869 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→70 Å / Num. obs: 20891 / % possible obs: 99.76 % / Redundancy: 12.6 % / Biso Wilson estimate: 31.7254807362 Å2 / Rmerge(I) obs: 0.08334 / Net I/σ(I): 20.86 |
Reflection shell | Resolution: 1.95→2.02 Å / Rmerge(I) obs: 1.142 / Num. unique obs: 2021 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7SEZ Resolution: 1.95000442951→69.995 Å / SU ML: 0.24573610686 / Cross valid method: FREE R-VALUE / σ(F): 1.34831509729 / Phase error: 24.8199895987
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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: 37.461745743 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95000442951→69.995 Å
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Refine LS restraints |
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LS refinement shell |
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