+Open data
-Basic information
Entry | Database: PDB / ID: 7bhy | ||||||
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Title | DNA-binding domain of DeoR in complex with the DNA operator | ||||||
Components |
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Keywords | DNA BINDING PROTEIN / Transcriptional repressor / Deoxyribose catabolism / Helix-turn-helix domain / Bacillus subtilis | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Novakova, M. / Rezacova, P. / Skerlova, J. / Brynda, J. | ||||||
Funding support | Czech Republic, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7bhy.cif.gz | 67 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7bhy.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 7bhy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7bhy_validation.pdf.gz | 450.7 KB | Display | wwPDB validaton report |
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Full document | 7bhy_full_validation.pdf.gz | 451.6 KB | Display | |
Data in XML | 7bhy_validation.xml.gz | 9.4 KB | Display | |
Data in CIF | 7bhy_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bh/7bhy ftp://data.pdbj.org/pub/pdb/validation_reports/bh/7bhy | HTTPS FTP |
-Related structure data
Related structure data | 7oykC 2w48S 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: DNA chain | Mass: 4589.006 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: It differs from the original operator sequence by missing DT10. Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
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#2: DNA chain | Mass: 4585.038 Da / Num. of mol.: 1 / Source method: obtained synthetically Details: It differs from the original operator sequence by missing DA6. Source: (synth.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) | ||||||
#3: Protein | Mass: 6601.396 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Details: SNAAS sequence is a cloning artefact. Source: (gene. exp.) Bacillus subtilis subsp. subtilis str. 168 (bacteria) Gene: deoR, yxxC, BSU39430 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P39140 #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.6 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.03 M NaNO3, 0.03 M Na2HPO4, 0.03 M (NH4)2SO4, 0.1 M Trizma base/bicine buffer system, pH 8.5, 12.5% (v/v) 2-methyl 2,4 pentanediol, 12.5% (v/v) PEG 1,000, and 12.5% (v/v) PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→43.34 Å / Num. obs: 17897 / % possible obs: 99.6 % / Redundancy: 10.86 % / Biso Wilson estimate: 56.336 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.151 / Χ2: 0.759 / Net I/σ(I): 14.08 / Num. measured all: 194360 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2W48 Resolution: 2.3→43.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.929 / SU R Cruickshank DPI: 0.2383 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.238 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 136.72 Å2 / Biso mean: 54.464 Å2 / Biso min: 30.82 Å2
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Refinement step | Cycle: final / Resolution: 2.3→43.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.356 Å / Rfactor Rfree error: 0
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