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Yorodumi- PDB-2dqr: Crystal structure of the replication terminator protein mutant RT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2dqr | ||||||
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Title | Crystal structure of the replication terminator protein mutant RTP.E39K.R42Q | ||||||
Components | Replication termination protein | ||||||
Keywords | DNA BINDING PROTEIN / DNA replication / winged-helix / RTP | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Vivian, J.P. / Wilce, J.A. / Wilce, M.C.J. | ||||||
Citation | Journal: to be published Title: Crystal structure of the replication terminator protein mutant RTP.E39K.R42Q Authors: Vivian, J.P. / 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 | 2dqr.cif.gz | 99.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2dqr.ent.gz | 78.6 KB | Display | PDB format |
PDBx/mmJSON format | 2dqr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dq/2dqr ftp://data.pdbj.org/pub/pdb/validation_reports/dq/2dqr | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The asymmetric unit contains two dimers. The biological unit is one dimer. |
-Components
#1: Protein | Mass: 14518.165 Da / Num. of mol.: 4 / Mutation: E39K,R42Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: rtp / Plasmid: pET-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68732, UniProt: P0CI76*PLUS #2: 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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 22% PEG 4000, 0.2M sodium acetate, 0.225M Tris HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 5, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→90 Å / Num. all: 12062 / Num. obs: 12062 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.142 |
Reflection shell | Resolution: 3→3.11 Å / Rmerge(I) obs: 0.69 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bm9_A (residues 72 to 88 omitted) Resolution: 3.01→25.45 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.87 / SU B: 38.83 / SU ML: 0.348 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.485 / 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: 39.157 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→25.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.01→3.087 Å / Total num. of bins used: 20
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