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Yorodumi- PDB-2i06: Escherichia Coli Replication Terminator Protein (Tus) Complexed W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i06 | ||||||
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Title | Escherichia Coli Replication Terminator Protein (Tus) Complexed With DNA- Locked form | ||||||
Components |
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Keywords | REPLICATION/DNA / PROTEIN-DNA COMPLEX / REPLICATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information replication fork arrest involved in DNA replication termination / DNA replication termination / sequence-specific DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Oakley, A.J. / Mulcair, M.D. / Schaeffer, P.M. / Dixon, N.E. | ||||||
Citation | Journal: To be Published Title: Polarity of Termination of DNA Replication in E. coli. Authors: Oakley, A.J. / Mulcair, M.D. / Schaeffer, P.M. / Dixon, N.E. #1: Journal: CELL(CAMBRIDGE,MASS.) / Year: 2006 Title: A molecular mousetrap determines polarity of termination of DNA replication in E. coli Authors: Mulcair, M.D. / Schaeffer, P.M. / Oakley, A.J. / Cross, H.F. / Neylon, C. / Hill, T.M. / Dixon, N.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2i06.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i06.ent.gz | 68.6 KB | Display | PDB format |
PDBx/mmJSON format | 2i06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/2i06 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i06 | HTTPS FTP |
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-Related structure data
Related structure data | 2ewjS 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
#1: DNA chain | Mass: 4856.191 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
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#2: DNA chain | Mass: 4927.225 Da / Num. of mol.: 1 / Source method: obtained synthetically | ||
#3: Protein | Mass: 35843.188 Da / Num. of mol.: 1 / Fragment: TUS Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tus / Plasmid: pCM847 / Production host: Escherichia coli (E. coli) / Strain (production host): AN1459 / References: UniProt: P16525 | ||
#4: Chemical | #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: 2.71 Å3/Da / Density % sol: 54.64 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.75 Details: 13% PEG 3350, 50mM Bis-Tris pH6.75, 200mM NaI, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||
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: 19-ID / Wavelength: 0.97929 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2006 Details: Rosenbaum-Rock monochromator, high-resolution double-crystal sagittal focusing, double crystal, Rosenbaum-Rock vertical focusing mirror |
Radiation | Monochromator: Rosenbaum-Rock / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97929 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 17442 / % possible obs: 64.6 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 5.1 % / Biso Wilson estimate: 26.833 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 25.52 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 4.04 / Num. unique all: 344 / Rsym value: 0.175 / % possible all: 13.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EWJ Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 25.679 / SU ML: 0.262 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 0.492 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: The crystals gave anisotropic diffraction, with stronger diffraction along c* than a*/b*. Thus completeness tends to fall off toward the high-resolution end.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.881 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.201→2.258 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 37.5427 Å / Origin y: 4.8955 Å / Origin z: 49.8063 Å
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