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Yorodumi- PDB-4pu8: Shewanella oneidensis Toxin Antitoxin System Antitoxin Protein Hi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4pu8 | ||||||
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Title | Shewanella oneidensis Toxin Antitoxin System Antitoxin Protein HipB Resolution 2.35 | ||||||
Components | Toxin-antitoxin system antidote transcriptional repressor Xre family | ||||||
Keywords | TOXIN / Toxin Antitoxin System | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Wen, Y. / Behiels, E. / Felix, J. / Elegheert, J. / Vergauwen, B. / Devreese, B. / Savvides, S. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2014 Title: The bacterial antitoxin HipB establishes a ternary complex with operator DNA and phosphorylated toxin HipA to regulate bacterial persistence. Authors: Wen, Y. / Behiels, E. / Felix, J. / Elegheert, J. / Vergauwen, B. / Devreese, B. / Savvides, S.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4pu8.cif.gz | 91.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4pu8.ent.gz | 71.8 KB | Display | PDB format |
PDBx/mmJSON format | 4pu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4pu8_validation.pdf.gz | 429.2 KB | Display | wwPDB validaton report |
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Full document | 4pu8_full_validation.pdf.gz | 429.1 KB | Display | |
Data in XML | 4pu8_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4pu8_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pu/4pu8 ftp://data.pdbj.org/pub/pdb/validation_reports/pu/4pu8 | HTTPS FTP |
-Related structure data
Related structure data | 4pu3C 4pu4C 4pu5C 4pu7C 3dnvS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 12951.791 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-4 / Gene: Shewmr4_3396, SO_0705 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EIX4 #2: Water | ChemComp-HOH / | |
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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: 1.59 Å3/Da / Density % sol: 22.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 7.5 Details: 0.1M Na HEPES pH7.5, 10% v/v 2-propanol, 20% PEG 4000, VAPOR DIFFUSION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.36 Å / Num. all: 45147 / Num. obs: 12674 / % possible obs: 99.71 % / Observed criterion σ(I): 2.15 |
-Processing
Software | Name: PHENIX / Version: (phenix.refine: dev_1287) / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3DNV Resolution: 2.35→38.36 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 22.82 / 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 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.35→38.36 Å
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Refine LS restraints |
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Refinement TLS params. | Method: refined / Origin x: 23.18 Å / Origin y: 21.3113 Å / Origin z: 34.0359 Å
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Refinement TLS group | Selection details: all |