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Yorodumi- PDB-6rnx: Crystal structure of the essential repressor DdrO from radiation-... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rnx | ||||||
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Title | Crystal structure of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti) | ||||||
Components | HTH-type transcriptional regulator DdrOC | ||||||
Keywords | DNA BINDING PROTEIN | ||||||
Function / homology | Helix-turn-helix / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / DNA-binding transcription factor activity / DNA binding / cytosol / HTH-type transcriptional regulator DdrOC Function and homology information | ||||||
Biological species | Deinococcus deserti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | ||||||
Authors | Arnoux, P. / Siponen, M.I. / Pignol, D. / De Groot, A. / Blanchard, L. | ||||||
Citation | Journal: Nucleic Acids Res. / Year: 2019 Title: Crystal structure of the transcriptional repressor DdrO: insight into the metalloprotease/repressor-controlled radiation response in Deinococcus. Authors: de Groot, A. / Siponen, M.I. / Magerand, R. / Eugenie, N. / Martin-Arevalillo, R. / Doloy, J. / Lemaire, D. / Brandelet, G. / Parcy, F. / Dumas, R. / Roche, P. / Servant, P. / Confalonieri, ...Authors: de Groot, A. / Siponen, M.I. / Magerand, R. / Eugenie, N. / Martin-Arevalillo, R. / Doloy, J. / Lemaire, D. / Brandelet, G. / Parcy, F. / Dumas, R. / Roche, P. / Servant, P. / Confalonieri, F. / Arnoux, P. / Pignol, D. / Blanchard, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6rnx.cif.gz | 135.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rnx.ent.gz | 90.6 KB | Display | PDB format |
PDBx/mmJSON format | 6rnx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rnx_validation.pdf.gz | 431.1 KB | Display | wwPDB validaton report |
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Full document | 6rnx_full_validation.pdf.gz | 435.1 KB | Display | |
Data in XML | 6rnx_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | 6rnx_validation.cif.gz | 14.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/6rnx ftp://data.pdbj.org/pub/pdb/validation_reports/rn/6rnx | HTTPS FTP |
-Related structure data
Related structure data | 6rmqSC 6rnzC 6ro6C S: Starting model for refinement C: citing same article (ref.) |
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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: 14758.857 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus deserti (strain VCD115 / DSM 17065 / LMG 22923) (bacteria) Strain: VCD115 / DSM 17065 / LMG 22923 / Gene: ddrOC, Deide_20570 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C1CYP4 #2: Chemical | ChemComp-CL / | #3: 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: 2.81 Å3/Da / Density % sol: 56.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Bis-Tris pH 5.5, 0.2 M Na-thiocyanate, 2.3 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Apr 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→50 Å / Num. obs: 8234 / % possible obs: 99 % / Redundancy: 9.6 % / Biso Wilson estimate: 66.53 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.6 |
Reflection shell | Resolution: 2.84→2.94 Å / Num. unique obs: 764 / CC1/2: 0.77 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RMQ Resolution: 2.84→49.81 Å / SU ML: 0.5939 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.6037 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 68.21 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.84→49.81 Å
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Refine LS restraints |
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LS refinement shell |
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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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