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Yorodumi- PDB-8pvz: Manganese-dependent transcriptional repressor DR2539 complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8pvz | |||||||||
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Title | Manganese-dependent transcriptional repressor DR2539 complexed with cadmium | |||||||||
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 / DNA binding Similarity search - Function | |||||||||
Biological species | Deinococcus radiodurans (radioresistant) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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. #1: Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams / Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8pvz.cif.gz | 149.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8pvz.ent.gz | 98.7 KB | Display | PDB format |
PDBx/mmJSON format | 8pvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/8pvz ftp://data.pdbj.org/pub/pdb/validation_reports/pv/8pvz | HTTPS FTP |
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-Related structure data
Related structure data | 8pvtC 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: 54.81 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 3% 6-Aminohexanoic acid; 0.1M Hepes pH 7.0; 1.2 M sodium acetate; 0.05M Cadmium sulphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97933 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 29, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97933 Å / Relative weight: 1 |
Reflection | Resolution: 2→46.92 Å / Num. obs: 24727 / % possible obs: 99.8 % / Redundancy: 5.5 % / Biso Wilson estimate: 35.33 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2→2.11 Å / Num. unique obs: 3534 / CC1/2: 0.622 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→43.6 Å / SU ML: 0.2513 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.7527 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: 41.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 86.1323728661 Å / Origin y: 60.4966891884 Å / Origin z: 12.6362827481 Å
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Refinement TLS group | Selection details: all |