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- PDB-2o5e: Structure of E. coli topoisomerase III in complex with an 8-base ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2o5e | ||||||
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Title | Structure of E. coli topoisomerase III in complex with an 8-base single stranded oligonucleotide. Frozen in glucose pH 7.0 | ||||||
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![]() | ISOMERASE/DNA / topoisomerase type IA complex with ssDNA / ISOMERASE-DNA COMPLEX | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Changela, A. / DiGate, R.J. / Mondragon, A. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 516.1 KB | Display | ![]() |
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PDB format | ![]() | 428.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2o19C ![]() 2o54C ![]() 2o59C ![]() 2o5cC ![]() 1d6mS ![]() 1i7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Details | Complex of E. coli topoisomerase III with DNA. Two molecules in the asymmetric unit in the same conformation. |
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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.) ![]() ![]() ![]() ![]() #3: Chemical | ChemComp-TDR / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.8 Å3/Da / Density % sol: 67.62 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1.5 M (NH4)SO4, 0.1M Sodium citrate, 0.5 NaCl, pH 7.0, 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: ![]() ![]() ![]() |
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: 2.5→29.132 Å / Num. obs: 79675 / % possible obs: 96.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 2.3 / Num. measured all: 14007 / Num. unique all: 5552 / Rsym value: 0.328 / % possible all: 93 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1D6M, 1I7D Resolution: 2.5→29.132 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 16.85 / SU ML: 0.199 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.312 / ESU R Free: 0.25 / 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: 45.063 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→29.132 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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