+Open data
-Basic information
Entry | Database: PDB / ID: 4g0w | ||||||
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Title | Human topoisomerase iibeta in complex with DNA and ametantrone | ||||||
Components |
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Keywords | ISOMERASE/DNA/ISOMERASE INHIBITOR / TOPRIM domain / winged-helix domain / coiled-coil domain / DNA-binding and cleavage / nucleus / ISOMERASE-DNA-ISOMERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information 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 / SUMOylation of DNA replication proteins / DNA topological change / 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 / SUMOylation of DNA replication proteins / DNA topological change / ribonucleoprotein complex binding / forebrain development / axonogenesis / B cell differentiation / neuron migration / cellular response to hydrogen peroxide / cellular senescence / ribonucleoprotein complex / chromatin binding / nucleolus / DNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.696 Å | ||||||
Authors | Wu, C.C. / Li, T.K. / Li, Y.C. / Chan, N.L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2013 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g0w.cif.gz | 328.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g0w.ent.gz | 253.3 KB | Display | PDB format |
PDBx/mmJSON format | 4g0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/4g0w ftp://data.pdbj.org/pub/pdb/validation_reports/g0/4g0w | HTTPS FTP |
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-Related structure data
Related structure data | 4g0uC 4g0vC 4j3nC 3qx3S 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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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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.) Homo sapiens (human) / Gene: TOP2B / Plasmid: PET51B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: Q02880, EC: 5.99.1.3 |
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-DNA chain , 2 types, 4 molecules CEDF
#2: DNA chain | Mass: 2436.619 Da / Num. of mol.: 2 / Source method: obtained synthetically #3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically |
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-Non-polymers , 3 types, 428 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.15 Å3/Da / Density % sol: 60.95 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.8 Details: 100mM magnesium acetate, 50mM 2-(N-morpholino)ethanesulfonic acid pH 5.8, 22% 2-methyl-2,4-pentanediol (MPD) , VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2012 |
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: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.696→30 Å / Num. all: 66542 / Num. obs: 65943 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 43.27 Å2 / Rsym value: 0.085 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 2.52 / Num. unique all: 3034 / Rsym value: 0.424 / % possible all: 91.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QX3 Resolution: 2.696→27.49 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8627 / SU ML: 0.39 / σ(F): 1.37 / Phase error: 21.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 33.162 Å2 / ksol: 0.306 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.16 Å2 / Biso mean: 44.8366 Å2 / Biso min: 11.52 Å2
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Refinement step | Cycle: LAST / Resolution: 2.696→27.49 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: 24
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