[English] 日本語
![](img/lk-miru.gif)
- PDB-6wdz: Porcine circovirus 2 Rep domain complexed with a single-stranded ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6wdz | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Porcine circovirus 2 Rep domain complexed with a single-stranded DNA 10-mer comprising the cleavage site | |||||||||
![]() |
| |||||||||
![]() | 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 | ![]() : / rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus ...: / rolling circle single-stranded viral DNA replication / endodeoxyribonuclease activity, producing 5'-phosphomonoesters / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / nucleotidyltransferase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA replication / RNA helicase activity / host cell nucleus / ATP hydrolysis activity / DNA binding / RNA binding / ATP binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Litzau, L.A. / Tompkins, K. / Shi, K. / Nelson, A. / Evans III, R.L. / Gordon, W.R. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() 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: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 101.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 73.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.6 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 480 KB | Display | |
Data in XML | ![]() | 17.4 KB | Display | |
Data in CIF | ![]() | 24.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6we0C ![]() 6we1C ![]() 5xorS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| |||||||||
2 | ![]()
| |||||||||
3 | ![]()
| |||||||||
4 | ![]()
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
#1: DNA chain | Mass: 3019.004 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #2: Protein | Mass: 13259.991 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.59 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1M Ammonium acetate, 25% Polyethylene glycol 3,350, 0.1M Bis-Tris pH 7 soaked in 25% glycerol for cryoprotectant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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: 2.03→43.1 Å / Num. obs: 26261 / % possible obs: 97.52 % / Redundancy: 2.9 % / Biso Wilson estimate: 25.87 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.06745 / Rpim(I) all: 0.04609 / Rrim(I) all: 0.08209 / Net I/σ(I): 12.49 |
Reflection shell | Resolution: 2.03→2.103 Å / Rmerge(I) obs: 0.3619 / Mean I/σ(I) obs: 3.63 / Num. unique obs: 2625 / CC1/2: 0.812 / CC star: 0.947 / Rpim(I) all: 0.2475 / Rrim(I) all: 0.4406 / % possible all: 98.17 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5xor + modeled 10-mer Resolution: 2.03→43.1 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.82 / 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: 97.07 Å2 / Biso mean: 32.539 Å2 / Biso min: 11.52 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.03→43.1 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17
|