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- PDB-4zsb: Crystal structure of the ligand-free effector-binding domain of D... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4zsb | ||||||
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Title | Crystal structure of the ligand-free effector-binding domain of DasR (DasR-EBD) | ||||||
![]() | HTH-type transcriptional repressor DasR | ||||||
![]() | TRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Effector-binding domain / N-acetylglucosamine utilization / Ligand-free / Master regulator | ||||||
Function / homology | ![]() DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / cytoplasm Similarity search - Function | ||||||
Biological species | Streptomyces coelicolor A3 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fillenberg, S.B. / Grau, F.C. / Muller, Y.A. | ||||||
Funding support | ![]()
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![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 47.5 KB | Display | ![]() |
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PDB format | ![]() | 32.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 424.3 KB | Display | ![]() |
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Full document | ![]() | 426.8 KB | Display | |
Data in XML | ![]() | 8.8 KB | Display | |
Data in CIF | ![]() | 11.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4zs8C ![]() 4zsiC ![]() 4zskC ![]() 2wv0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 19028.689 Da / Num. of mol.: 1 / Fragment: UNP residues 89-254 Source method: isolated from a genetically manipulated source Details: DasR-EBD comprises residues 88-254 of full-length DasR Source: (gene. exp.) ![]() Gene: dasR, SCO5231, SC7E4.28c / Production host: ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.77 Å3/Da / Density % sol: 55.67 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Bis-Tris propane pH 9.0, 4.0 M potassium formate, 20 % (w/v) PEG monomethyl ether 2,000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-225 / Detector: CCD / Date: Feb 2, 2011 |
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→50 Å / Num. obs: 14018 / % possible obs: 98.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 17.5 |
Reflection shell | Resolution: 2→2.08 Å / Redundancy: 3 % / Rmerge(I) obs: 0.806 / Mean I/σ(I) obs: 1.4 / % possible all: 94.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: Effector-binding domain of entry 2wv0 Resolution: 2.004→44.727 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.21 / Phase error: 28.46 / 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: 2.004→44.727 Å
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Refine LS restraints |
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LS refinement shell |
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