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Open data
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Basic information
Entry | Database: PDB / ID: 7oyk | |||||||||
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Title | DNA-binding domain of CggR in complex with the DNA operator | |||||||||
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![]() | DNA BINDING PROTEIN / Transcriptional repressor / Glycolysis / Helix-turn-helix domain / Bacillus subtilis | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Novakova, M. / Rezacova, P. / Skerlova, J. / Brynda, J. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insight into DNA recognition by bacterial transcriptional regulators of the SorC/DeoR family. Authors: Soltysova, M. / Sieglova, I. / Fabry, M. / Brynda, J. / Skerlova, J. / Rezacova, P. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 141.2 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 4 molecules AAADDDCCCBBB
#1: Protein | Mass: 11121.280 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: The first amino-acid residues "SNAAS" are remnants after the cleavage of the His-tag by TEV protease. Source: (gene. exp.) ![]() ![]() Gene: cggR, yvbQ, BSU33950 / Plasmid: pET151/D-TOPO / Production host: ![]() ![]() |
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-DNA operator - strand ... , 2 types, 6 molecules EEELLLGGGFFFKKKHHH
#2: DNA chain | Mass: 4885.209 Da / Num. of mol.: 3 / Source method: obtained synthetically Source: (synth.) ![]() ![]() #3: DNA chain | Mass: 4911.173 Da / Num. of mol.: 3 / Source method: obtained synthetically Source: (synth.) ![]() ![]() |
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-Non-polymers , 4 types, 144 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/EDO.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | ChemComp-EDO / | #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.53 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 10% (w/v) PEG 3350, 100mM MES, pH 6.5, 100mM calcium chloride, 13% (v/v) glycerol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2020 |
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 34417 / % possible obs: 96.8 % / Redundancy: 2.3 % / Biso Wilson estimate: 46.7 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2.1→2.23 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 10673 / CC1/2: 0.514 / Rrim(I) all: 1.111 / % possible all: 95.4 |
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Processing
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Refinement | Method to determine structure: ![]() Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.543 Å2
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Refinement step | Cycle: LAST / Resolution: 2.101→45.837 Å
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Refine LS restraints |
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LS refinement shell |
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