+Open data
-Basic information
Entry | Database: PDB / ID: 7r5a | ||||||
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Title | Vibrio cholera ParD2:ParE2 antitoxin:toxin complex | ||||||
Components |
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Keywords | TOXIN / Prokaryotic Toxin:Antitoxin System / intrinsically disordered proteins / RHH protein / DNA binding protein / transcriptional repressor / Antitoxin / Gyrase-poison / Vibrio cholerae | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.95 Å | ||||||
Authors | Garcia-Rodriguez, G. / Loris, R. | ||||||
Funding support | 1items
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Citation | Journal: Sci Adv / Year: 2024 Title: Toxin:antitoxin ratio sensing autoregulation of the Vibrio cholerae parDE2 module. Authors: Garcia-Rodriguez, G. / Girardin, Y. / Kumar Singh, R. / Volkov, A.N. / Van Dyck, J. / Muruganandam, G. / Sobott, F. / Charlier, D. / Loris, R. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2021 Title: Entropic pressure controls the oligomerization of the Vibrio cholerae ParD2 antitoxin. Authors: Garcia-Rodriguez, G. / Girardin, Y. / Volkov, A.N. / Singh, R.K. / Muruganandam, G. / Van Dyck, J. / Sobott, F. / Versees, W. / Charlier, D. / Loris, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7r5a.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7r5a.ent.gz | 93 KB | Display | PDB format |
PDBx/mmJSON format | 7r5a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7r5a_validation.pdf.gz | 451.7 KB | Display | wwPDB validaton report |
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Full document | 7r5a_full_validation.pdf.gz | 457.2 KB | Display | |
Data in XML | 7r5a_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 7r5a_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r5/7r5a ftp://data.pdbj.org/pub/pdb/validation_reports/r5/7r5a | HTTPS FTP |
-Related structure data
Related structure data | 3kxeS S: Starting model for refinement |
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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
#1: Protein | Mass: 12435.160 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Gene: VC_A0359 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KMJ0 |
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#2: Protein | Mass: 8972.801 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria) Gene: parD, VC_A0360.1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P58093 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.75 Å3/Da / Density % sol: 29.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M Potassium chloride, 0.1 M Sodium HEPES, pH 7, 15 % PEG 5000 MME |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978565 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 15, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978565 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→46.51 Å / Num. obs: 78228 / % possible obs: 99.81 % / Redundancy: 12.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.1628 / Net I/σ(I): 10.62 |
Reflection shell | Resolution: 2.95→3.056 Å / Num. unique obs: 7628 / CC1/2: 0.512 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3kxe Resolution: 2.95→46.51 Å / SU ML: 0.46 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 32.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 218.72 Å2 / Biso mean: 98.0618 Å2 / Biso min: 43.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→46.51 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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