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Open data
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Basic information
Entry | Database: PDB / ID: 1d3y | ||||||
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Title | STRUCTURE OF THE DNA TOPOISOMERASE VI A SUBUNIT | ||||||
![]() | DNA TOPOISOMERASE VI A SUBUNIT | ||||||
![]() | ISOMERASE / TOPOISOMERASE VI / DNA BINDING PROTEIN / SPO11 HOMOLOG | ||||||
Function / homology | ![]() DNA endonuclease activity, producing 3'-phosphomonoesters / : / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA unwinding involved in DNA replication / DNA topological change / chromosome / magnesium ion binding / DNA binding / ATP binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() | ||||||
![]() | Nichols, M.D. / DeAngelis, K.A. / Keck, J.L. / Berger, J.M. | ||||||
![]() | ![]() Title: Structure and function of an archaeal topoisomerase VI subunit with homology to the meiotic recombination factor Spo11. Authors: Nichols, M.D. / DeAngelis, K. / Keck, J.L. / Berger, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 131.9 KB | Display | ![]() |
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PDB format | ![]() | 102.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 376 KB | Display | ![]() |
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Full document | ![]() | 386.7 KB | Display | |
Data in XML | ![]() | 13.3 KB | Display | |
Data in CIF | ![]() | 21.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 34098.785 Da / Num. of mol.: 2 / Fragment: DNA BINDING CORE / Mutation: DELETED NONCONSERVED N-TERMINAL RESIDUES 1-69 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Plasmid: PET24B / Production host: ![]() ![]() References: UniProt: TOP6A_METJA, UniProt: Q57815*PLUS, EC: 5.99.1.3 #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.9 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: PEG 8000, MPD, NA-CACODYLATE, MGCL2, NACL, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. all: 45432 / Num. obs: 43773 / % possible obs: 96.5 % / Redundancy: 8.8 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2→2.07 Å / Rmerge(I) obs: 0.131 / % possible all: 93.6 |
Reflection shell | *PLUS % possible obs: 93.6 % |
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Processing
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Refinement | Resolution: 2→20 Å / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.197 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: p_bond_d / Dev ideal: 0.006 |