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Yorodumi- PDB-2o5c: Structure of E. coli topoisomerase III in complex with an 8-base ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2o5c | ||||||
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Title | Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 5.5 | ||||||
Components |
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Keywords | ISOMERASE/DNA / topoisomerase type IA complex with ssDNA / ISOMERASE-DNA COMPLEX | ||||||
Function / homology | Function and homology information cytoplasmic replication fork / sequence-specific single stranded DNA binding / chromosome separation / DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / DNA topological change / DNA-templated DNA replication / DNA recombination / DNA repair / magnesium ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Changela, A. / DiGate, R.J. / Mondragon, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Structural Studies of E. coli Topoisomerase III-DNA Complexes Reveal a Novel Type IA Topoisomerase-DNA Conformational Intermediate. Authors: Changela, A. / Digate, R.J. / Mondragon, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2o5c.cif.gz | 521.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2o5c.ent.gz | 432.1 KB | Display | PDB format |
PDBx/mmJSON format | 2o5c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o5/2o5c ftp://data.pdbj.org/pub/pdb/validation_reports/o5/2o5c | HTTPS FTP |
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-Related structure data
Related structure data | 2o19C 2o54C 2o59C 2o5eC 1d6mS 1i7dS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Details | Complex of E. coli topoisomerase III with DNA. Two molecules in the asymmetric unit in the same conformation |
-Components
#1: DNA chain | Mass: 2386.593 Da / Num. of mol.: 2 / Source method: obtained synthetically #2: Protein | Mass: 74151.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: topB / Production host: Escherichia coli (E. coli) / References: UniProt: P14294, DNA topoisomerase #3: Chemical | ChemComp-TDR / | #4: Chemical | #5: 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: 3.78 Å3/Da / Density % sol: 67.45 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 M NaCl, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.9479 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9479 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→29.147 Å / Num. obs: 95028 / % possible obs: 96.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.35→2.41 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 3.6 / Num. measured all: 9173 / Num. unique all: 5343 / Rsym value: 0.215 / % possible all: 74.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1D6M, 1I7D Resolution: 2.35→29.147 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.027 / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.239 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.855 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→29.147 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.35→2.411 Å / Total num. of bins used: 20
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