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Yorodumi- PDB-6rmq: Crystal structure of a selenomethionine-substituted A70M I84M mut... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rmq | ||||||
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Title | Crystal structure of a selenomethionine-substituted A70M I84M mutant 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 / SAD / Resolution: 3 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 | 6rmq.cif.gz | 58.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rmq.ent.gz | 46.5 KB | Display | PDB format |
PDBx/mmJSON format | 6rmq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rmq_validation.pdf.gz | 436.2 KB | Display | wwPDB validaton report |
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Full document | 6rmq_full_validation.pdf.gz | 438.3 KB | Display | |
Data in XML | 6rmq_validation.xml.gz | 11 KB | Display | |
Data in CIF | 6rmq_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/6rmq ftp://data.pdbj.org/pub/pdb/validation_reports/rm/6rmq | HTTPS FTP |
-Related 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: 14977.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Deinococcus deserti (bacteria) / Gene: ddrOC, Deide_20570 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: C1CYP4 #2: 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: 2.91 Å3/Da / Density % sol: 57.79 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 3.5 M Ammonium Chloride 0.1 M Bis-Tris propane pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 13, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 3→76 Å / Num. obs: 7531 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 3→3.3 Å / Num. unique obs: 1193 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 3→76 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.834 / SU B: 18.346 / SU ML: 0.333 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.768 Å2
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Refinement step | Cycle: 1 / Resolution: 3→76 Å
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Refine LS restraints |
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