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Yorodumi- PDB-2i05: Escherichia Coli Replication Terminator Protein (Tus) Complexed W... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2i05 | ||||||
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Title | Escherichia Coli Replication Terminator Protein (Tus) Complexed With TerA DNA | ||||||
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: 2.6 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 | 2i05.cif.gz | 94.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2i05.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 2i05.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2i05_validation.pdf.gz | 444.3 KB | Display | wwPDB validaton report |
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Full document | 2i05_full_validation.pdf.gz | 465.3 KB | Display | |
Data in XML | 2i05_validation.xml.gz | 16.1 KB | Display | |
Data in CIF | 2i05_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/i0/2i05 ftp://data.pdbj.org/pub/pdb/validation_reports/i0/2i05 | HTTPS FTP |
-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: 2.76 Å3/Da / Density % sol: 55.44 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12.5% PEG 3350, 50mM Bis-Tris pH6.5, 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: 2.6→50 Å / Num. obs: 13969 / % possible obs: 82 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Redundancy: 5.2 % / Biso Wilson estimate: 56.028 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.088 / Net I/σ(I): 28.36 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.259 / Mean I/σ(I) obs: 3.1 / Num. unique all: 421 / Rsym value: 0.259 / % possible all: 25.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2EWJ Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.87 / SU B: 29.777 / SU ML: 0.287 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -2 / ESU R: 1.345 / ESU R Free: 0.429 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 53.288 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.668 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 38.127 Å / Origin y: 4.4711 Å / Origin z: 50.221 Å
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