+Open data
-Basic information
Entry | Database: PDB / ID: 7epj | |||||||||
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Title | Crystal structure of E.coli CcdB mutant V46L | |||||||||
Components | Toxin CcdB | |||||||||
Keywords | TOXIN / CcdB / Topoisomerase poison / global suppressor | |||||||||
Function / homology | Function and homology information DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) inhibitor activity / negative regulation of DNA-templated DNA replication / toxin-antitoxin complex / plasmid maintenance / transcription repressor complex / negative regulation of DNA-templated transcription Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.354 Å | |||||||||
Authors | Manjunath, K. / Goyal, P. / Varadarajan, R. | |||||||||
Funding support | India, 2items
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Citation | Journal: Plos Genet. / Year: 2022 Title: Mechanistic insights into global suppressors of protein folding defects. Authors: Chattopadhyay, G. / Bhowmick, J. / Manjunath, K. / Ahmed, S. / Goyal, P. / Varadarajan, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7epj.cif.gz | 41.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7epj.ent.gz | 24.8 KB | Display | PDB format |
PDBx/mmJSON format | 7epj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7epj ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epj | HTTPS FTP |
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-Related structure data
Related structure data | 7epgC 7epiC 3vubS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 11735.535 Da / Num. of mol.: 1 / Mutation: V46L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ccdB, G, letB, letD, ECOK12F043 / Plasmid: pBAD24 / Production host: Escherichia coli (E. coli) / Strain (production host): Top10Gyrase / References: UniProt: P62554 | ||||
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#2: Chemical | #3: 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: 1.92 Å3/Da / Density % sol: 36 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 200mM CaCl2, 25% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.0358 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0358 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→33.98 Å / Num. obs: 19433 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 5.8 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.043 / Rrim(I) all: 0.108 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.288 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 2799 / CC1/2: 0.928 / Rpim(I) all: 0.141 / Rrim(I) all: 0.322 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VUB Resolution: 1.354→33.979 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.159 / SU B: 0.907 / SU ML: 0.038 / Average fsc free: 0.9456 / Average fsc work: 0.9501 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.058 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: 9.358 Å2
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Refinement step | Cycle: LAST / Resolution: 1.354→33.979 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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