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Yorodumi- PDB-7kij: Muscovy duck circovirus Rep domain complexed with a single-strand... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7kij | |||||||||
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Title | Muscovy duck circovirus Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site | |||||||||
Components |
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Keywords | REPLICATION/DNA / HUH-tag / HUH motif / Rep domain / viral protein / single stranded DNA / ssDNA / ssDNA binding / REPLICATION / DNA BINDING PROTEIN / REPLICATION-DNA complex | |||||||||
Function / homology | Function and homology information : / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / nucleotidyltransferase activity / DNA replication / RNA helicase activity / RNA binding Similarity search - Function | |||||||||
Biological species | Muscovy duck circovirus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | |||||||||
Authors | Tompkins, K.J. / Gordon, W.R. / Shi, K. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Mbio / Year: 2023 Title: Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases. Authors: Smiley, A.T. / Tompkins, K.J. / Pawlak, M.R. / Krueger, A.J. / Evans 3rd, R.L. / 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 | 7kij.cif.gz | 122.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7kij.ent.gz | 92 KB | Display | PDB format |
PDBx/mmJSON format | 7kij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7kij_validation.pdf.gz | 467.3 KB | Display | wwPDB validaton report |
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Full document | 7kij_full_validation.pdf.gz | 467.8 KB | Display | |
Data in XML | 7kij_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 7kij_validation.cif.gz | 20.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/7kij ftp://data.pdbj.org/pub/pdb/validation_reports/ki/7kij | HTTPS FTP |
-Related structure data
Related structure data | 7kiiC 7kikC 6wdzS 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 on special symmetry positions |
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-Components
-Protein / DNA chain , 2 types, 4 molecules CADB
#1: Protein | Mass: 12385.729 Da / Num. of mol.: 2 / Mutation: Y91F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Muscovy duck circovirus / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D2JZX8 #2: DNA chain | Mass: 2993.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Muscovy duck circovirus |
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-Non-polymers , 4 types, 287 molecules
#3: Chemical | ChemComp-GOL / | ||||
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#4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MN / | #6: Water | ChemComp-HOH / | |
-Details
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: 3.44 Å3/Da / Density % sol: 64.26 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 0.1 M sodium acetate, pH 4.8, 2.2M ammonium sulfate, 20% glycerol added to drop |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 27, 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: 1.69→54.65 Å / Num. obs: 48935 / % possible obs: 99.84 % / Redundancy: 8.7 % / Biso Wilson estimate: 28.27 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03628 / Rpim(I) all: 0.01275 / Rrim(I) all: 0.03856 / Net I/σ(I): 32.89 |
Reflection shell | Resolution: 1.69→1.751 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.8253 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 4791 / CC1/2: 0.784 / CC star: 0.938 / Rpim(I) all: 0.2922 / Rrim(I) all: 0.8776 / % possible all: 99.69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6WDZ Resolution: 1.69→54.65 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.5 / 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: 87.21 Å2 / Biso mean: 34.3287 Å2 / Biso min: 20.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.69→54.65 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
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