[English] 日本語
![](img/lk-miru.gif)
- PDB-8df8: Structure of M. kandleri topoisomerase V in complex with DNA. 40 ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8df8 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of M. kandleri topoisomerase V in complex with DNA. 40 base pair symmetric DNA complex | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / Topoisomerase V Type IC / Abasic DNA / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Osterman, A. / Mondragon, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism. Authors: Osterman, A. / Mondragon, A. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 478.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 309.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 8df7SC ![]() 8df9C ![]() 8dfbC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Unit cell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 97110.445 Da / Num. of mol.: 2 / Mutation: K809A, K820A, K831A, K835A, K846A, K851A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
---|
-DNA chain , 2 types, 2 molecules UV
#2: DNA chain | Mass: 12915.303 Da / Num. of mol.: 1 / Mutation: GUA U13 is an abasic site / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#3: DNA chain | Mass: 12946.312 Da / Num. of mol.: 1 / Mutation: GUA V13 is an abasic site / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 10 molecules ![](data/chem/img/K.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PO3.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/PO3.gif)
#4: Chemical | ChemComp-K / #5: Chemical | ChemComp-PO4 / #6: Chemical | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.14 Å3/Da / Density % sol: 70.29 % / Description: Box-like |
---|---|
Crystal grow | Temperature: 303 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. ...Details: Protein was mixed with the annealed oligonucleotide using a stoichiometric ratio of 1.25:1 DNA to protein in 1X DNA binding buffer. Reactions were incubated for thirty minutes at 65 C. Crystals started to appear within minutes of setting up the trays in 1:1 or 2:1 well to complex ratio. Well solution: 2 ul:1 ul (reaction:well solution), 2% PEG 8K, 24 mM sodium acetate pH 5.1, 26 mM sodium acetate pH 5.6, 12.5 uM phosphotungstic acid. 5X DNA binding buffer: 250 mM sodium acetate pH 5.0 at 65C, 150 mM sodium chloride, 5 mM magnesium chloride. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 4, 2020 / Details: Monochromator |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→108.8 Å / Num. obs: 56136 / % possible obs: 69 % / Redundancy: 13.9 % / Biso Wilson estimate: 96.2 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Rrim(I) all: 0.084 / Net I/σ(I): 21 |
Reflection shell | Resolution: 2.92→3.24 Å / Redundancy: 18.7 % / Rmerge(I) obs: 1.605 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 51701 / CC1/2: 0.744 / Rrim(I) all: 1.65 / % possible all: 12.9 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 8DF7 Resolution: 2.92→58.76 Å / SU ML: 0.3946 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 36.4552 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 98.65 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.92→58.76 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|