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Yorodumi- PDB-8qa8: Crystal structure of the C-terminally truncated transcriptional r... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8qa8 | ||||||||||||
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Title | Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S | ||||||||||||
Components | Transcriptional repressor protein KorB | ||||||||||||
Keywords | DNA BINDING PROTEIN / multi-drug resistance / ParABS / clamp / CTP switch / DNA segregation / gene expression regulation | ||||||||||||
Function / homology | Function and homology information 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 | Escherichia coli (E. coli) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||||||||
Authors | McLean, T.C. / Mundy, J.E.A. / Lawson, D.M. / Le, T.B.K. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: To Be Published Title: Crystal structure of the C-terminally truncated transcriptional repressor protein KorB from the RK2 plasmid complexed with CTP-gamma-S 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8qa8.cif.gz | 505 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8qa8.ent.gz | 415.2 KB | Display | PDB format |
PDBx/mmJSON format | 8qa8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8qa8_validation.pdf.gz | 2.2 MB | Display | wwPDB validaton report |
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Full document | 8qa8_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 8qa8_validation.xml.gz | 45.2 KB | Display | |
Data in CIF | 8qa8_validation.cif.gz | 61.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qa/8qa8 ftp://data.pdbj.org/pub/pdb/validation_reports/qa/8qa8 | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 26418.576 Da / Num. of mol.: 6 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.) Escherichia coli (E. coli) / Gene: korB / Plasmid: pET21b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07674 #2: Chemical | ChemComp-CTP / #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9179 Å |
Detector | Type: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Mar 2, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9179 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→198.27 Å / Num. obs: 80304 / % possible obs: 100 % / Redundancy: 13.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.236 / Rpim(I) all: 0.067 / Rrim(I) all: 0.245 / Χ2: 0.43 / Net I/σ(I): 7.9 / Num. measured all: 1069894 |
Reflection shell | Resolution: 2.3→2.35 Å / % possible obs: 100 % / Redundancy: 11.1 % / Rmerge(I) obs: 1.887 / Num. measured all: 50482 / Num. unique obs: 4563 / CC1/2: 0.718 / Rpim(I) all: 0.594 / Rrim(I) all: 1.979 / Χ2: 0.18 / Net I/σ(I) obs: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→121.28 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / SU B: 20.803 / SU ML: 0.225 / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.721 Å2
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Refinement step | Cycle: 1 / Resolution: 2.3→121.28 Å
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