+Open data
-Basic information
Entry | Database: PDB / ID: 7vg8 | ||||||
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Title | TYLCV Rep-DNA | ||||||
Components |
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Keywords | VIRAL PROTEIN / complex | ||||||
Function / homology | Function and homology information endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / DNA replication / host cell nucleus / structural molecule activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Tomato yellow leaf curl virus Tomato yellow leaf curl virus-IL [MX: SLP:11] | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å | ||||||
Authors | Zhang, S.Y. / Wang, C.N. | ||||||
Funding support | China, 1items
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Citation | Journal: To Be Published Title: structure of TYLCV Rep complexed with ssDNA Authors: Zhang, S.Y. / Wang, C.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vg8.cif.gz | 54.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vg8.ent.gz | 28.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vg/7vg8 ftp://data.pdbj.org/pub/pdb/validation_reports/vg/7vg8 | HTTPS FTP |
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-Related structure data
Related structure data | 6we0S S: Starting model for refinement |
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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
#1: Protein | Mass: 13093.854 Da / Num. of mol.: 1 / Mutation: Y101F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato yellow leaf curl virus / Gene: AC1 / Production host: prokaryote coculture (bacteria) References: UniProt: A0A286LJ32, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters |
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#2: DNA chain | Mass: 2713.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Tomato yellow leaf curl virus-IL [MX: SLP:11] Production host: DNA satellites (virus) |
#3: Chemical | ChemComp-MN / |
#4: 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: 2.95 Å3/Da / Density % sol: 58.37 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.1M Bis-Tris pH 6.5, 28%w/v Polyethylene glyco monomethyl ether 2000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 10, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→21.5 Å / Num. obs: 11179 / % possible obs: 93.96 % / Redundancy: 6 % / Biso Wilson estimate: 26.16 Å2 / CC1/2: 0.99 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.04→2.11 Å / Num. unique obs: 1028 / CC1/2: 0.72 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WE0 Resolution: 2.04→21.5 Å / SU ML: 0.2437 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2802 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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: 27.12 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.04→21.5 Å
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Refine LS restraints |
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LS refinement shell |
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