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Yorodumi- PDB-2a0i: F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a0i | ||||||
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Title | F Factor TraI Relaxase Domain bound to F oriT Single-stranded DNA | ||||||
Components |
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Keywords | hydrolase/DNA / single-stranded DNA / protein-DNA complex / 5-strand antiparallel beta sheet / hydrolase-DNA COMPLEX | ||||||
Function / homology | Function and homology information DNA topoisomerase / DNA topoisomerase type I (single strand cut, ATP-independent) activity / metabolic process / DNA helicase activity / DNA helicase / ATP hydrolysis activity / DNA binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.72 Å | ||||||
Authors | Larkin, C. / Datta, S. / Harley, M.J. / Anderson, B.J. / Ebie, A. / Hargreaves, V. / Schildbach, J.F. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Inter- and intramolecular determinants of the specificity of single-stranded DNA binding and cleavage by the f factor relaxase. Authors: Larkin, C. / Datta, S. / Harley, M.J. / Anderson, B.J. / Ebie, A. / Hargreaves, V. / Schildbach, J.F. #1: Journal: Structure / Year: 2003 Title: Structural insights into single-stranded DNA binding and cleavage by F factor TraI Authors: Datta, S. / Larkin, C. / Schildbach, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a0i.cif.gz | 80.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a0i.ent.gz | 57.1 KB | Display | PDB format |
PDBx/mmJSON format | 2a0i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a0i ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a0i | HTTPS FTP |
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-Related structure data
Related structure data | 1p4dS 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 on special symmetry positions |
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-Components
#1: DNA chain | Mass: 6932.430 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthesized oligonucleotide |
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#2: Protein | Mass: 36326.547 Da / Num. of mol.: 1 / Mutation: Y16F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: traI / Plasmid: pET-24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P14565, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-IMD / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.08 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 1000, Imidazole, Calcium Chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
Components of the solutions |
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 31, 2003 |
Radiation | Monochromator: MSC/Max-Flux confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.72→99 Å / Num. obs: 9891 / % possible obs: 87.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.048 / Χ2: 0.74 |
Reflection shell | Resolution: 2.72→2.82 Å / % possible obs: 62.2 % / Rmerge(I) obs: 0.331 / Num. measured obs: 671 / Χ2: 0.715 / % possible all: 62.2 |
-Phasing
Phasing MR | Method rotation: fast direct / Method translation: &STRIP%trans_method |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1P4D Chain A Resolution: 2.72→14.87 Å / Rfactor Rfree error: 0.009 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS bulk solvent model used / Bsol: 42.3338 Å2 / ksol: 0.256485 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.05 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.72→14.87 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Xplor file |
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