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Yorodumi- PDB-7bcb: Crystal structure of the HTH DNA binding protein ArdK from R388 p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7bcb | |||||||||
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Title | Crystal structure of the HTH DNA binding protein ArdK from R388 plasmid bound to IR3 DNA | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / Helix Turn Helix / Direct repeat / Plasmid conjugation | |||||||||
Function / homology | : / TrfB transcriptional repressor protein / TrfB plasmid transcriptional repressor / RNA polymerase sigma factor, region 3/4-like / DNA / DNA (> 10) / TrfB transcriptional repressor protein domain-containing protein Function and homology information | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Fernandez-Lopez, R. / Boer, D.R. / Moncalian, G. | |||||||||
Funding support | Spain, 2items
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Citation | Journal: Nucleic Acids Res. / Year: 2022 Title: Structural basis of direct and inverted DNA sequence repeat recognition by helix-turn-helix transcription factors. Authors: Fernandez-Lopez, R. / Ruiz, R. / Del Campo, I. / Gonzalez-Montes, L. / Boer, D.R. / de la Cruz, F. / Moncalian, G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bcb.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bcb.ent.gz | 49.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/7bcb ftp://data.pdbj.org/pub/pdb/validation_reports/bc/7bcb | HTTPS FTP |
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-Related structure data
Related structure data | 7bbqC 7bcaSC 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
#1: Protein | Mass: 12518.110 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: R388 plasmid / Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Plasmid: pET29c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6I6B7 #2: DNA chain | | Mass: 5522.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) #3: DNA chain | | Mass: 5504.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
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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: 58.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 20% 10,000 polyethylene glycol, 0.1 M HEPES pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9792 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→77.22 Å / Num. obs: 12277 / % possible obs: 98.3 % / Redundancy: 8.1 % / Biso Wilson estimate: 61.38 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.102 / Net I/σ(I): 4.6 |
Reflection shell | Resolution: 2.6→2.74 Å / Rmerge(I) obs: 0.362 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 1744 / CC1/2: 0.94 / Rrim(I) all: 0.446 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BCA Resolution: 2.8→45.89 Å / SU ML: 0.504 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.7723 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.08 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→45.89 Å
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Refine LS restraints |
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LS refinement shell |
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