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- PDB-8qa9: Crystal structure of the RK2 plasmid encoded co-complex of the C-... -
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Open data
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Basic information
Entry | Database: PDB / ID: 8qa9 | ||||||||||||
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Title | Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA | ||||||||||||
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![]() | DNA BINDING PROTEIN / multi-drug resistance / ParABS / clamp / CTP switch / DNA segregation / gene expression regulation | ||||||||||||
Function / homology | ![]() positive regulation of sporulation resulting in formation of a cellular spore / chromosome segregation / chromosome / negative regulation of DNA-templated transcription / protein-containing complex / DNA binding / identical protein binding Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | McLean, T.C. / Mundy, J.E.A. / Lawson, D.M. / Le, T.B.K. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of the RK2 plasmid encoded co-complex of the C-terminally truncated transcriptional repressor protein KorB complexed with the partner repressor protein KorA bound to OA-DNA Authors: McLean, T.C. / Mundy, J.E.A. / Lawson, D.M. / Le, T.B.K. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 295.4 KB | Display | ![]() |
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PDB format | ![]() | 237.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.2 MB | Display | ![]() |
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Full document | ![]() | 2.2 MB | Display | |
Data in XML | ![]() | 23.9 KB | Display | |
Data in CIF | ![]() | 33.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26418.576 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The crystallised sequence corresponds to residues 30-253 of the full 358-residue wild-type sequence appended with a C-terminal hexa-histidine tag via a short linker sequence KLAAALE. Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein | Mass: 12850.631 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: The crystallised sequence corresponds to the full-length 101-residue wild-type KorA protein appended with a C-terminal hexa-histidine tag via a short linker sequence KLAAALE. Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: DNA chain | Mass: 4278.815 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Synthetic short double-stranded DNA sequence containing the KorA binding motif OA Source: (synth.) ![]() ![]() #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.12 Å3/Da / Density % sol: 61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 14, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→82.65 Å / Num. obs: 29438 / % possible obs: 100 % / Redundancy: 12.4 % / Biso Wilson estimate: 58.1 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.039 / Rrim(I) all: 0.135 / Χ2: 0.59 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 2.7→2.83 Å / % possible obs: 100 % / Redundancy: 11.6 % / Rmerge(I) obs: 1.533 / Num. measured all: 45107 / Num. unique obs: 3879 / CC1/2: 0.677 / Rpim(I) all: 0.473 / Rrim(I) all: 1.606 / Χ2: 0.21 / Net I/σ(I) obs: 1 |
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Processing
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Refinement | Method to determine structure: ![]()
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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 mean: 76.613 Å2
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Refinement step | Cycle: 1 / Resolution: 2.7→82.65 Å
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