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- PDB-5jub: Crystal structure of ComR from S.thermophilus in complex with DNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5jub | ||||||
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Title | Crystal structure of ComR from S.thermophilus in complex with DNA and its signalling peptide ComS. | ||||||
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![]() | TRANSCRIPTION / RNPP / Transcriptional activator / TPR domain / HTH domain / quorum-sensor / competence regulator | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Talagas, A. / Fontaine, L. / Ledesma-Garcia, L. / Li de la Sierra-Gallay, I. / Hols, P. / Nessler, S. | ||||||
![]() | ![]() Title: Structural Insights into Streptococcal Competence Regulation by the Cell-to-Cell Communication System ComRS. Authors: Talagas, A. / Fontaine, L. / Ledesma-Garca, L. / Mignolet, J. / Li de la Sierra-Gallay, I. / Lazar, N. / Aumont-Nicaise, M. / Federle, M.J. / Prehna, G. / Hols, P. / Nessler, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 152.1 KB | Display | ![]() |
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PDB format | ![]() | 118.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 458.3 KB | Display | ![]() |
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Full document | ![]() | 464.4 KB | Display | |
Data in XML | ![]() | 22.1 KB | Display | |
Data in CIF | ![]() | 29.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36547.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() #2: Protein/peptide | Mass: 883.066 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cognate signalling peptide of ComR Source: (synth.) ![]() #3: DNA chain | | Mass: 6141.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ComR-box from ComX promoter Source: (synth.) ![]() #4: DNA chain | | Mass: 6122.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ComR-box from ComX promoter Source: (synth.) ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % |
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Crystal grow | Temperature: 290.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% PEG 550MME, 0.1M MgCl2, 0,05M Tris-HCl, pH=8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978563 Å / Relative weight: 1 |
Reflection | Resolution: 2.57→46.553 Å / Num. obs: 27134 / % possible obs: 99 % / Redundancy: 5.3 % / CC1/2: 0.99 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.31 |
Reflection shell | Resolution: 2.57→2.63 Å / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 1.81 / % possible all: 98.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: ComR apo Resolution: 2.57→46.553 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 31.21 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→46.553 Å
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Refine LS restraints |
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LS refinement shell |
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