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Yorodumi- PDB-1pvg: Crystal Structure of the ATPase region of Saccharomyces Cerevisia... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pvg | ||||||
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Title | Crystal Structure of the ATPase region of Saccharomyces Cerevisiae topoisomerase II | ||||||
Components | DNA topoisomerase IIDNA gyrase | ||||||
Keywords | ISOMERASE / GHKL ATPase domain | ||||||
Function / homology | Function and homology information replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity ...replication fork progression beyond termination site / DNA replication termination region / chromatin remodeling at centromere / regulation of mitotic recombination / sister chromatid segregation / resolution of meiotic recombination intermediates / SUMOylation of DNA replication proteins / synaptonemal complex / reciprocal meiotic recombination / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA strand elongation involved in DNA replication / rRNA transcription / DNA topological change / chromatin organization / mitochondrion / DNA binding / ATP binding / identical protein binding / metal ion binding / nucleus Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Classen, S. / Olland, S. / Berger, J.M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: Structure of the topoisomerase II ATPase region and its mechanism of inhibition by the chemotherapeutic agent ICRF-187 Authors: Classen, S. / Olland, S. / Berger, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvg.cif.gz | 177.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvg.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 1pvg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvg ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dimer |
-Components
#1: Protein | Mass: 48567.883 Da / Num. of mol.: 2 / Fragment: N-terminal ATPase region Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: TOP2 / Plasmid: pET28b-TEV-ScT2ATPase / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus / References: UniProt: P06786, EC: 5.99.1.3 #2: Chemical | #3: Chemical | #4: 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: 2.31 Å3/Da / Density % sol: 46.77 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: microbatch under oil / pH: 6.5 Details: PEG 1500, Potassium Chloride, Glycerol, Sodium Cacodylate, pH 6.5, microbatch under oil, temperature 293K | ||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: unknown | ||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.127, 0.9796 | |||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2002 | |||||||||
Radiation | Monochromator: Silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→30 Å / Num. all: 76036 / Num. obs: 75706 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 27.502 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 22 | |||||||||
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6077 / Rsym value: 0.43 / % possible all: 72.7 | |||||||||
Reflection | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / Num. measured all: 1143715 | |||||||||
Reflection shell | *PLUS % possible obs: 72.7 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→29.75 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.931 / SU B: 3.183 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.43 / ESU R: 0.161 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 23.666 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→29.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20 /
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 8.5 % / Rfactor Rfree: 0.241 / Rfactor Rwork: 0.206 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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