+Open data
-Basic information
Entry | Database: PDB / ID: 7epi | |||||||||
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Title | Crystal structure of E.coli CcdB mutant S60E | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.931 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 | 7epi.cif.gz | 39 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7epi.ent.gz | 23.4 KB | Display | PDB format |
PDBx/mmJSON format | 7epi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/7epi ftp://data.pdbj.org/pub/pdb/validation_reports/ep/7epi | HTTPS FTP |
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-Related structure data
Related structure data | 7epgC 7epjC 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: 11763.544 Da / Num. of mol.: 1 / Mutation: S60E 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: 1.9 Å3/Da / Density % sol: 35.23 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1 / Details: 200mM CaCl2, 10% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 30, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→10 Å / Num. obs: 6557 / % possible obs: 97.5 % / Redundancy: 3.4 % / Biso Wilson estimate: 8.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.081 / Rrim(I) all: 0.154 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.93→2.03 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 890 / CC1/2: 0.801 / Rpim(I) all: 0.268 / Rrim(I) all: 0.504 / % possible all: 91.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VUB Resolution: 1.931→9.996 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.151 / SU B: 3.531 / SU ML: 0.102 / Average fsc free: 0.9302 / Average fsc work: 0.9486 / Cross valid method: FREE R-VALUE / ESU R: 0.202 / ESU R Free: 0.162 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: 10.319 Å2
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Refinement step | Cycle: LAST / Resolution: 1.931→9.996 Å
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Refine LS restraints |
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LS refinement shell |
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