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Yorodumi- PDB-8a0w: Crystal structure of the HigA2 antitoxin in complex with operator DNA -
+Open data
-Basic information
Entry | Database: PDB / ID: 8a0w | |||||||||
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Title | Crystal structure of the HigA2 antitoxin in complex with operator DNA | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN / antitoxin / HigA2 / repressor / toxin-antitoxin module | |||||||||
Function / homology | Antitoxin MqsA/HigA-2 / Antitoxin component of bacterial toxin-antitoxin system, MqsA / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA binding / PHOSPHATE ION / DNA / DNA (> 10) / Antitoxin HigA-2 Function and homology information | |||||||||
Biological species | Vibrio cholerae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.334 Å | |||||||||
Authors | Hadzi, S. / Loris, R. | |||||||||
Funding support | Slovenia, Belgium, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Fuzzy recognition by the prokaryotic transcription factor HigA2 from Vibrio cholerae. Authors: Hadzi, S. / Zivic, Z. / Kovacic, M. / Zavrtanik, U. / Haeserts, S. / Charlier, D. / Plavec, J. / Volkov, A.N. / Lah, J. / Loris, R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8a0w.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8a0w.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 8a0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/8a0w ftp://data.pdbj.org/pub/pdb/validation_reports/a0/8a0w | HTTPS FTP |
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-Related structure data
Related structure data | 5j9iS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 11581.993 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: higA-2, VC_A0469 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9KMA5 #2: DNA chain | | Mass: 5234.382 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria) #3: DNA chain | | Mass: 5181.376 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Vibrio cholerae (bacteria) #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 4.7 Å3/Da / Density % sol: 73.84 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.2 M sodium chloride, 0.1 M Na HEPES pH 7.5, 12%(w/v) PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 24, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→49.26 Å / Num. obs: 27228 / % possible obs: 99.2 % / Redundancy: 10.3 % / Rrim(I) all: 0.078 / Net I/σ(I): 18.15 |
Reflection shell | Resolution: 2.33→2.47 Å / Mean I/σ(I) obs: 2.02 / Num. unique obs: 4150 / Rrim(I) all: 0.793 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5J9I Resolution: 2.334→49.259 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 2.05 / Phase error: 20.36 / 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: 122.7 Å2 / Biso mean: 59.8119 Å2 / Biso min: 33.64 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.334→49.259 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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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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