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Yorodumi- PDB-8pvt: Manganese-dependent transcriptional repressor DR2539 complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pvt | |||||||||
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Title | Manganese-dependent transcriptional repressor DR2539 complexed with cadmium (SAD 7 keV) | |||||||||
Components | Iron dependent repressor, putative | |||||||||
Keywords | DNA BINDING PROTEIN / Transcriptional regulator | |||||||||
Function / homology | Function and homology information transition metal ion binding / protein dimerization activity / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans (radioresistant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å | |||||||||
Authors | Mota, C. / De Sanctis, D. | |||||||||
Funding support | Portugal, 2items
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Citation | Journal: Febs J. / Year: 2024 Title: Metal ion activation and DNA recognition by the Deinococcus radiodurans manganese sensor DR2539. Authors: Mota, C. / Webster, M. / Saidi, M. / Kapp, U. / Zubieta, C. / Giachin, G. / Manso, J.A. / de Sanctis, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pvt.cif.gz | 79.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pvt.ent.gz | 48.1 KB | Display | PDB format |
PDBx/mmJSON format | 8pvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/8pvt ftp://data.pdbj.org/pub/pdb/validation_reports/pv/8pvt | HTTPS FTP |
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-Related structure data
Related structure data | 8pvzC 8pw0C 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
#1: Protein | Mass: 15921.969 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus radiodurans (radioresistant) Gene: DR_2539 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRF3 #2: Chemical | ChemComp-CD / #3: 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: 2.72 Å3/Da / Density % sol: 54.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.1 M Hepes pH 7.0; 1.2 M sodium acetate; 0.05 M Cadmium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7712 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.7712 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→43.6 Å / Num. obs: 12916 / % possible obs: 99.4 % / Redundancy: 23.2 % / Biso Wilson estimate: 38.04 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2.5→2.64 Å / Num. unique obs: 1752 / CC1/2: 0.869 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.5→43.59 Å / SU ML: 0.327 / Cross valid method: FREE R-VALUE / σ(F): 0.68 / Phase error: 25.6713 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.35 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→43.59 Å
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Refine LS restraints |
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LS refinement shell |
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