+Open data
-Basic information
Entry | Database: PDB / ID: 4g0u | ||||||
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Title | Human topoisomerase IIbeta in complex with DNA and amsacrine | ||||||
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 / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 | 4g0u.cif.gz | 323.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g0u.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 4g0u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g0u_validation.pdf.gz | 1003 KB | Display | wwPDB validaton report |
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Full document | 4g0u_full_validation.pdf.gz | 1017.7 KB | Display | |
Data in XML | 4g0u_validation.xml.gz | 51.9 KB | Display | |
Data in CIF | 4g0u_validation.cif.gz | 74 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/4g0u ftp://data.pdbj.org/pub/pdb/validation_reports/g0/4g0u | HTTPS FTP |
-Related structure data
Related structure data | 4g0vC 4g0wC 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, 434 molecules
#4: Chemical | ChemComp-MG / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.1 Å3/Da / Density % sol: 60.27 % |
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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: BL13C1 / Wavelength: 0.97622 Å |
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 23, 2011 |
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: 2.7→30 Å / Num. all: 65343 / Num. obs: 63644 / % possible obs: 97.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Biso Wilson estimate: 42.71 Å2 / Rsym value: 0.08 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.7→2.75 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.467 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3232 / Rsym value: 0.467 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3QX3 Resolution: 2.7→28.231 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8606 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 21.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 131.29 Å2 / Biso mean: 31.152 Å2 / Biso min: 6.38 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→28.231 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: 23
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