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Yorodumi- PDB-4zsi: Crystal structure of the effector-binding domain of DasR (DasR-EB... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4zsi | ||||||
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Title | Crystal structure of the effector-binding domain of DasR (DasR-EBD) in complex with glucosamine-6-phosphate | ||||||
Components | HTH-type transcriptional repressor DasR | ||||||
Keywords | TRANSCRIPTION / Repressor / Bacterial transcription regulation / Transcription factor / GntR/HutC family / Effector-binding domain / N-acetylglucosamine utilization / Master regulator / Glucosamine-6-phosphate | ||||||
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 A3 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.652 Å | ||||||
Authors | Fillenberg, S.B. / Koerner, S. / 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 | 4zsi.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4zsi.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 4zsi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4zsi_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 4zsi_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 4zsi_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 4zsi_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zs/4zsi ftp://data.pdbj.org/pub/pdb/validation_reports/zs/4zsi | HTTPS FTP |
-Related structure data
Related structure data | 4zs8C 4zsbC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 19157.867 Da / Num. of mol.: 2 / Fragment: UNP residues 88-254 Source method: isolated from a genetically manipulated source Details: DasR-EBD comprises residues 88-254 of full-length DasR Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria) Gene: dasR, SCO5231, SC7E4.28c / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K492 #2: Sugar | ChemComp-GLP / | #3: Chemical | #4: Sugar | ChemComp-4R1 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.81 % |
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Crystal grow | Temperature: 292.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M potassium thiocyanate and 30 % (w/v) PEG monomethyl ether 2,000 |
-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: 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: 1.65→35 Å / Num. obs: 46439 / % possible obs: 99.8 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.65→1.71 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.812 / Mean I/σ(I) obs: 2.1 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Effector-binding domain of entry 2wv0 Resolution: 1.652→27.133 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.16 / 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: 1.652→27.133 Å
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Refine LS restraints |
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LS refinement shell |
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