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Open data
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Basic information
Entry | Database: PDB / ID: 4j3n | ||||||
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Title | Human Topoisomerase Iibeta in complex with DNA | ||||||
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![]() | ISOMERASE/DNA / TOPRIM DOMAIN / WINGED-HELIX DOMAIN / COILED-COIL DOMAIN / DNA BINDING AND CLEAVAGE / NUCLEUS / ISOMERASE-DNA COMPLEX | ||||||
Function / homology | ![]() positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding ...positive regulation of single stranded viral RNA replication via double stranded DNA intermediate / sister chromatid segregation / resolution of meiotic recombination intermediates / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / cellular response to ATP / positive regulation of double-strand break repair via nonhomologous end joining / DNA topological change / SUMOylation of DNA replication proteins / ribonucleoprotein complex binding / forebrain development / B cell differentiation / axonogenesis / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / nucleus / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, C.C. / Li, T.K. / Li, Y.C. / Chan, N.L. | ||||||
![]() | ![]() Title: On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs Authors: Wu, C.C. / Li, Y.C. / Wang, Y.R. / Li, T.K. / Chan, N.L. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 333.3 KB | Display | ![]() |
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PDB format | ![]() | 256.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 481.7 KB | Display | ![]() |
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Full document | ![]() | 505.6 KB | Display | |
Data in XML | ![]() | 56.7 KB | Display | |
Data in CIF | ![]() | 81.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4g0uC ![]() 4g0vC ![]() 4g0wC ![]() 3l4kS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 91928.367 Da / Num. of mol.: 2 / Fragment: HTOP2BETA CLEAVAGE CORE, UNP RESIDUES 450-1206 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: DNA chain | Mass: 2436.619 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE OLIGONUCLEOTIDE SEQUENCE 5'-AGCCGAGCTGCAGCTCGGCT-3' WAS ORDERED FROM VIOGENE. #3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: THE OLIGONUCLEOTIDE SEQUENCE 5'-AGCCGAGCTGCAGCTCGGCT-3' WAS ORDERED FROM VIOGENE. #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Sequence details | THE SEQUENCE OF DNA USED IN THE EXPERIMENT WAS 5'-AGCCGAGCTGCAGCTCGGCT-3'. AND THE DNAS WERE ...THE SEQUENCE OF DNA USED IN THE EXPERIMENT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 0.1M MAGNESIUM ACETATE, 50MM 2-(N-MORPHOLINO)ETHANESULFONIC ACID PH 5.8, 22% 2-METHYL-2,4-PENTANEDIOL (MPT), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 25, 2010 |
Radiation | Monochromator: HORIZONTALLY FOCUSING SINGLE CRYSTAL MONOCHROMATOR (CRYSTAL TYPE SI(1 1 1)) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97622 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. all: 109988 / Num. obs: 103829 / % possible obs: 94.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Rsym value: 0.06 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 2.3→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5259 / Rsym value: 0.489 / % possible all: 94.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3L4K Resolution: 2.3→27.31 Å / Occupancy max: 1 / Occupancy min: 0.12 / SU ML: 0.28 / σ(F): 1.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.53 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 139.83 Å2 / Biso mean: 46.3339 Å2 / Biso min: 18.33 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→27.31 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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