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Yorodumi- PDB-6we1: Wheat dwarf virus Rep domain complexed with a single-stranded DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6we1 | ||||||
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Title | Wheat dwarf virus Rep domain complexed with a single-stranded DNA 8-mer comprising the cleavage site | ||||||
Components |
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Keywords | REPLICATION/DNA / HUH-tag / HUH motif / replicase / viral protein / single stranded DNA / ssDNA / ssDNA binding / REPLICATION / DNA BINDING PROTEIN / REPLICATION-DNA complex | ||||||
Function / homology | Function and homology information rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / host cell nucleus / structural molecule activity / DNA binding ...rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / nucleotidyltransferase activity / helicase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / host cell nucleus / structural molecule activity / DNA binding / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Wheat dwarf virus | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.612 Å | ||||||
Authors | Tompkins, K. / Litzau, L.A. / Pornschloegl, L. / Nelson, A.T. / Evans III, R.L. / Gordon, W.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2021 Title: Molecular underpinnings of ssDNA specificity by Rep HUH-endonucleases and implications for HUH-tag multiplexing and engineering. Authors: Tompkins, K.J. / Houtti, M. / Litzau, L.A. / Aird, E.J. / Everett, B.A. / Nelson, A.T. / Pornschloegl, L. / Limon-Swanson, L.K. / Evans, R.L. / Evans, K. / Shi, K. / Aihara, H. / Gordon, W.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6we1.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6we1.ent.gz | 48.6 KB | Display | PDB format |
PDBx/mmJSON format | 6we1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6we1_validation.pdf.gz | 441.6 KB | Display | wwPDB validaton report |
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Full document | 6we1_full_validation.pdf.gz | 443.1 KB | Display | |
Data in XML | 6we1_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 6we1_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/6we1 ftp://data.pdbj.org/pub/pdb/validation_reports/we/6we1 | HTTPS FTP |
-Related structure data
Related structure data | 6wdzC 6we0C 6q1mS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15836.812 Da / Num. of mol.: 2 / Mutation: Y106F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wheat dwarf virus / Gene: rep / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A0F6N3D1, UniProt: Q67622*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters #2: DNA chain | Mass: 2409.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Wheat dwarf virus #3: Chemical | #4: 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: 2.44 Å3/Da / Density % sol: 49.7 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% w/v PEG 8000, 0.1 M sodium cocadylate, pH 6.5, 0.2M zinc acetate, 25% glycerol |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 29, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 2.612→28.55 Å / Num. obs: 9674 / % possible obs: 93.29 % / Redundancy: 1.6 % / Biso Wilson estimate: 53.18 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.071 / Rrim(I) all: 0.112 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 2.612→2.705 Å / Mean I/σ(I) obs: 2.27 / Num. unique obs: 876 / CC1/2: 0.702 / CC star: 0.908 / Rpim(I) all: 0.378 / Rrim(I) all: 0.609 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6q1m Resolution: 2.612→28.55 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.28 / Stereochemistry target values: ML
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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 max: 89.39 Å2 / Biso mean: 47.1581 Å2 / Biso min: 25.85 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.612→28.55 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
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