+Open data
-Basic information
Entry | Database: PDB / ID: 2efw | ||||||
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Title | Crystal structure of the RTP:nRB complex from Bacillus subtilis | ||||||
Components |
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Keywords | REPLICATION/DNA / protein-DNA complex / 'winged'-helix protein / DNA replication termination / replication fork arrest / REPLICATION-DNA COMPLEX | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Vivian, J.P. / Porter, C.J. / Wilce, J.A. / Wilce, M.C.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: An asymmetric structure of the Bacillus subtilis replication terminator protein in complex with DNA Authors: Vivian, J.P. / Porter, C.J. / Wilce, J.A. / Wilce, M.C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2efw.cif.gz | 143.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2efw.ent.gz | 109.6 KB | Display | PDB format |
PDBx/mmJSON format | 2efw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ef/2efw ftp://data.pdbj.org/pub/pdb/validation_reports/ef/2efw | HTTPS FTP |
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-Related structure data
Related structure data | 1f4kS 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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2 |
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Unit cell |
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-Components
#1: DNA chain | Mass: 6397.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the B site sequence of TerI #2: DNA chain | Mass: 6486.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: the B site sequence of TerI #3: Protein | Mass: 14531.099 Da / Num. of mol.: 4 / Mutation: C110S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rtp / Plasmid: pET-9 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68732, UniProt: P0CI76*PLUS #4: 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: 2.97 Å3/Da / Density % sol: 58.54 % | ||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 2% PEG 4000, 125mM sodium acetate, pH 4.6, 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: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 32161 / % possible obs: 94.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 2.3 / % possible all: 84.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1F4K (with residues 72 to 88 and the DNA removed) Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.855 / SU B: 31.275 / SU ML: 0.321 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.349 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.106 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→50 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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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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