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Yorodumi- PDB-4xr2: Escherichia Coli Replication Terminator Protein (Tus) H114A mutan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xr2 | ||||||||||||
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Title | Escherichia Coli Replication Terminator Protein (Tus) H114A mutant Complexed With DNA- TerA lock. | ||||||||||||
Components |
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Keywords | REPLICATION/DNA / DNA complex / replication / Tus / Ter / 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: 2.35 Å | ||||||||||||
Authors | Oakley, A.J. | ||||||||||||
Funding support | Australia, 3items
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Citation | Journal: Nature / Year: 2015 Title: Replisome speed determines the efficiency of the Tus-Ter replication termination barrier. Authors: Elshenawy, M.M. / Jergic, S. / Xu, Z.Q. / Sobhy, M.A. / Takahashi, M. / Oakley, A.J. / Dixon, N.E. / Hamdan, S.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xr2.cif.gz | 178.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xr2.ent.gz | 137 KB | Display | PDB format |
PDBx/mmJSON format | 4xr2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/4xr2 ftp://data.pdbj.org/pub/pdb/validation_reports/xr/4xr2 | HTTPS FTP |
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-Related structure data
Related structure data | 4xr0C 4xr1C 4xr3C 2i05S 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 36736.191 Da / Num. of mol.: 1 / Mutation: H144A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: tus, tau, b1610, JW1602 / Plasmid: pCM862 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P16525 |
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-DNA chain , 2 types, 2 molecules BC
#2: DNA chain | Mass: 4856.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: TerA / Source: (synth.) Escherichia coli (E. coli) |
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#3: DNA chain | Mass: 4927.225 Da / Num. of mol.: 1 / Mutation: A328G, G329A / Source method: obtained synthetically / Source: (synth.) Escherichia coli (E. coli) |
-Non-polymers , 4 types, 73 molecules
#4: Chemical | #5: Chemical | ChemComp-MPD / ( | #6: Chemical | ChemComp-EDO / | #7: 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: 2.81 Å3/Da / Density % sol: 56.16 % / Description: bipyramids |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 8-12% (v/v) PEG 3350, 100 mM NaI, 50 mM Bis-Tris / PH range: 6.2 - 6.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 15, 2014 |
Radiation | Monochromator: 0.9537 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→75 Å / Num. obs: 23147 / % possible obs: 99.6 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.856 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2I05 Resolution: 2.35→62.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 22.083 / SU ML: 0.244 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.243 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.033 Å2
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Refinement step | Cycle: 1 / Resolution: 2.35→62.74 Å
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Refine LS restraints |
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