+Open data
-Basic information
Entry | Database: PDB / ID: 4zs8 | ||||||
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Title | Crystal structure of ligand-free, full length DasR | ||||||
Components | HTH-type transcriptional repressor DasR | ||||||
Keywords | TRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Winged helix-turn-helix motif / N-acetylglucosamine utilization / Ligand-free / Master regulator | ||||||
Function / homology | Function and homology information DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Fillenberg, S.B. / Muller, Y.A. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Plos One / Year: 2016 Title: Crystal Structures of the Global Regulator DasR from Streptomyces coelicolor: Implications for the Allosteric Regulation of GntR/HutC Repressors. Authors: Fillenberg, S.B. / Friess, M.D. / Korner, S. / Bockmann, R.A. / Muller, Y.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4zs8.cif.gz | 102.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zs8.ent.gz | 78.9 KB | Display | PDB format |
PDBx/mmJSON format | 4zs8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zs8 ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zs8 | HTTPS FTP |
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-Related structure data
Related structure data | 4zsbC 4zsiC 4zskC 2wv0S 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: 28666.664 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria) Strain: ATCC BAA-471 / A3(2) / M145 / Gene: dasR, SCO5231, SC7E4.28c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K492 #2: Chemical | ChemComp-EDO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.54 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M sodium citrate tribasic dihydrate pH 5.5, 26 % (w/v) PEG 400, 10 % (v/v) isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Dec 4, 2010 |
Radiation | Monochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 17696 / % possible obs: 99.9 % / Redundancy: 8 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 21.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.03 / Mean I/σ(I) obs: 2.2 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: DNA- and effector-binding domains of entry 2wv0 Resolution: 2.6→44.522 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 26.78 / 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: 2.6→44.522 Å
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Refine LS restraints |
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LS refinement shell |
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