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Yorodumi- PDB-6rnz: Crystal structure of the N-terminal HTH DNA-binding domain of the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rnz | ||||||
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Title | Crystal structure of the N-terminal HTH DNA-binding domain of the essential repressor DdrO from radiation-resistant Deinococcus bacteria (Deinococcus deserti) | ||||||
Components | HTH-type transcriptional regulator DdrOC | ||||||
Keywords | DNA BINDING PROTEIN / ---- | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Deinococcus deserti (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Arnoux, P. / Siponen, M.I. / Pignol, D. / Brandelet, G. / 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 | 6rnz.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rnz.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 6rnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/6rnz ftp://data.pdbj.org/pub/pdb/validation_reports/rn/6rnz | HTTPS FTP |
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-Related structure data
Related structure data | 6rmqC 6rnxSC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 7512.542 Da / Num. of mol.: 2 / Fragment: N-terminus Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus deserti (bacteria) / Gene: ddrOC, Deide_20570 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: C1CYP4 #2: Chemical | #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: 2.42 Å3/Da / Density % sol: 49.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1 M Bis-Tris propane pH 7, 2.5 M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→44 Å / Num. obs: 31092 / % possible obs: 98.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.35→1.4 Å / Num. unique obs: 2968 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6RNX Resolution: 1.35→43.94 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.038 / SU ML: 0.036 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.675 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→43.94 Å
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Refine LS restraints |
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