[English] 日本語
Yorodumi- PDB-6we0: Wheat dwarf virus Rep domain complexed with a single-stranded DNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6we0 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Wheat dwarf virus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site | |||||||||
Components |
| |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Tompkins, K. / Litzau, L.A. / Shi, K. / Nelson, A. / Evans III, R.L. / Gordon, W.R. | |||||||||
Funding support | United States, 2items
| |||||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6we0.cif.gz | 77.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6we0.ent.gz | 52.3 KB | Display | PDB format |
PDBx/mmJSON format | 6we0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6we0_validation.pdf.gz | 1.9 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6we0_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 6we0_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 6we0_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/we/6we0 ftp://data.pdbj.org/pub/pdb/validation_reports/we/6we0 | HTTPS FTP |
-Related structure data
Related structure data | 6wdzC 6we1C 6q1mS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15594.540 Da / Num. of mol.: 1 / Mutation: Y106F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wheat dwarf virus / Gene: repA / Production host: Escherichia coli BL21 (bacteria) References: UniProt: A7KQY4, UniProt: Q67622*PLUS, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters | ||||
---|---|---|---|---|---|
#2: DNA chain | Mass: 3003.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Wheat dwarf 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 |
---|
-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.33 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop 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: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→41.34 Å / Num. obs: 15366 / % possible obs: 95.23 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.51 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.07455 / Rrim(I) all: 0.08357 / Net I/σ(I): 14.17 |
Reflection shell | Resolution: 1.8→1.864 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.8513 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 1551 / CC1/2: 0.571 / CC star: 0.852 / Rrim(I) all: 0.9629 / % possible all: 98.54 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6Q1M Resolution: 1.8→41.34 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.26 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 74.28 Å2 / Biso mean: 29.4686 Å2 / Biso min: 15.96 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.8→41.34 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: 4.465 Å / Origin y: 14.5582 Å / Origin z: 10.5412 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|