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Yorodumi- PDB-5gwi: Structure of a Human topoisomerase IIbeta fragment in complex wit... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5gwi | |||||||||
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Title | Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R | |||||||||
Components |
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Keywords | ISOMERASE/DNA/ISOMERASE INHIBITOR / Type II topoisomerase / Anti-cancer drug / TopoII cleavage complex / ISOMERASE-DNA complex / 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 / 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 | Homo sapiens (human) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.737 Å | |||||||||
Authors | Wang, Y.R. / Chen, S.F. / Wu, C.C. / Chan, N.L. | |||||||||
Citation | Journal: Nucleic Acids Res. / Year: 2017 Title: Producing irreversible topoisomerase II-mediated DNA breaks by site-specific Pt(II)-methionine coordination chemistry Authors: Wang, Y.R. / Chen, S.F. / Wu, C.C. / Liao, Y.W. / Lin, T.S. / Liu, K.T. / Chen, Y.S. / Li, T.K. / Chien, T.C. / 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 | 5gwi.cif.gz | 323.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5gwi.ent.gz | 248 KB | Display | PDB format |
PDBx/mmJSON format | 5gwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5gwi_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5gwi_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 5gwi_validation.xml.gz | 50.6 KB | Display | |
Data in CIF | 5gwi_validation.cif.gz | 68.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/5gwi ftp://data.pdbj.org/pub/pdb/validation_reports/gw/5gwi | HTTPS FTP |
-Related structure data
Related structure data | 5gwjC 5gwkC 3qx3S C: citing same article (ref.) S: Starting model for refinement |
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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: 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 BL21(DE3) (bacteria) / Strain (production host): BL21(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 / Source: (synth.) synthetic construct (others) #3: DNA chain | Mass: 3654.378 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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-Non-polymers , 4 types, 193 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-MG / #7: Water | ChemComp-HOH / | |
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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: 3.17 Å3/Da / Density % sol: 61.17 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Magnesium Acetate, 2-(N-morpholino)ethanesulfonic, 2-methyl-2,4-pentanediol |
-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: Sep 19, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.737→29.724 Å / Num. obs: 62539 / % possible obs: 98.2 % / Redundancy: 3.6 % / CC1/2: 0.815 / Rsym value: 0.469 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 2.74→2.84 Å / Mean I/σ(I) obs: 3.03 / CC1/2: 0.815 / Rpim(I) all: 0.29 / Rsym value: 0.469 / Χ2: 1.004 / % possible all: 96.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3QX3 Resolution: 2.737→29.724 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.737→29.724 Å
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Refine LS restraints |
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LS refinement shell |
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