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Yorodumi- PDB-6kmq: 2.3 Angstrom resolution structure of dimeric HigBA toxin-antitoxi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kmq | ||||||
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Title | 2.3 Angstrom resolution structure of dimeric HigBA toxin-antitoxin complex from E. coli | ||||||
Components |
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Keywords | TOXIN/ANTITOXIN / Toxin-antitoxin complex / HigBA / endoribonuclease / protein-protein complex / PROTEIN BINDING | ||||||
Function / homology | Function and homology information toxin-antitoxin complex / regulation of growth / core promoter sequence-specific DNA binding / regulation of mRNA stability / RNA endonuclease activity / Hydrolases; Acting on ester bonds / negative regulation of translation / regulation of DNA-templated transcription / protein homodimerization activity / RNA binding Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Jadhav, P. / Sinha, V.K. / Rothweiler, U. / Singh, M. | ||||||
Funding support | India, 1items
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Citation | Journal: Biochem.J. / Year: 2020 Title: 2.09 angstrom Resolution structure of E. coli HigBA toxin-antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin. Authors: Jadhav, P.V. / Sinha, V.K. / Chugh, S. / Kotyada, C. / Bachhav, D. / Singh, R. / Rothweiler, U. / Singh, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kmq.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kmq.ent.gz | 69.5 KB | Display | PDB format |
PDBx/mmJSON format | 6kmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kmq_validation.pdf.gz | 436.5 KB | Display | wwPDB validaton report |
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Full document | 6kmq_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 6kmq_validation.xml.gz | 9.1 KB | Display | |
Data in CIF | 6kmq_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/6kmq ftp://data.pdbj.org/pub/pdb/validation_reports/km/6kmq | HTTPS FTP |
-Related structure data
Related structure data | 6kmlC 5ifgS 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: 13676.759 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: higB, ygjN, b3083, JW3054 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P64578, Hydrolases; Acting on ester bonds |
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#2: Protein | Mass: 15008.354 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: higA, ygjM, b3082, JW3053 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P67701 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.76 Å3/Da / Density % sol: 30.07 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 0.05M MgCl2, 0.2M KCl, 0.1M Tris pH 7.5, 20% PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 27, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→28.492 Å / Num. obs: 8815 / % possible obs: 97.5 % / Redundancy: 3.75 % / CC1/2: 0.999 / Net I/σ(I): 13.16 |
Reflection shell | Resolution: 2.3→2.309 Å / Num. unique obs: 1421 / CC1/2: 0.887 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IFG Resolution: 2.35→28.492 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 38.48
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 121.36 Å2 / Biso mean: 67.778 Å2 / Biso min: 36.22 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.35→28.492 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 97 %
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Refinement TLS params. | Method: refined / Origin x: 8.7668 Å / Origin y: 1.4319 Å / Origin z: 11.0338 Å
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Refinement TLS group |
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