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Yorodumi- PDB-5jub: Crystal structure of ComR from S.thermophilus in complex with DNA... -
+Open data
-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. | ||||||
Components |
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Keywords | TRANSCRIPTION / RNPP / Transcriptional activator / TPR domain / HTH domain / quorum-sensor / competence regulator | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptococcus thermophilus LMD-9 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | ||||||
Authors | Talagas, A. / Fontaine, L. / Ledesma-Garcia, L. / Li de la Sierra-Gallay, I. / Hols, P. / Nessler, S. | ||||||
Citation | Journal: PLoS Pathog. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jub.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jub.ent.gz | 118.5 KB | Display | PDB format |
PDBx/mmJSON format | 5jub.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5jub_validation.pdf.gz | 458.3 KB | Display | wwPDB validaton report |
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Full document | 5jub_full_validation.pdf.gz | 464.4 KB | Display | |
Data in XML | 5jub_validation.xml.gz | 22.1 KB | Display | |
Data in CIF | 5jub_validation.cif.gz | 29.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ju/5jub ftp://data.pdbj.org/pub/pdb/validation_reports/ju/5jub | HTTPS FTP |
-Related 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: 36547.996 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus thermophilus LMD-9 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: A0A1L1QK15*PLUS #2: Protein/peptide | Mass: 883.066 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Cognate signalling peptide of ComR Source: (synth.) Streptococcus thermophilus LMD-9 (bacteria) #3: DNA chain | | Mass: 6141.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ComR-box from ComX promoter Source: (synth.) Streptococcus thermophilus LMD-9 (bacteria) #4: DNA chain | | Mass: 6122.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: ComR-box from ComX promoter Source: (synth.) Streptococcus thermophilus LMD-9 (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: 2.45 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: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.978563 Å |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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