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Yorodumi- PDB-6cqk: Crystal Structure of mitochondrial single-stranded DNA binding pr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cqk | ||||||
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Title | Crystal Structure of mitochondrial single-stranded DNA binding proteins from S. cerevisiae, Rim1 (Form1) | ||||||
Components | SsDNA-binding protein essential for mitochondrial genome maintenance | ||||||
Keywords | DNA BINDING PROTEIN / Mitochondrial single-stranded DNA binding proteins / Rim1 | ||||||
Function / homology | Function and homology information positive regulation of mitochondrial DNA replication / mitochondrial DNA replication / mitochondrial genome maintenance / mitochondrial nucleoid / single-stranded DNA binding / mitochondrion Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Singh, S.P. / Kukshal, V. / Bona, P.D. / Lytle, A.K. / Edwin, A. / Galletto, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nucleic Acids Res. / Year: 2018 Title: The mitochondrial single-stranded DNA binding protein from S. cerevisiae, Rim1, does not form stable homo-tetramers and binds DNA as a dimer of dimers. Authors: Singh, S.P. / Kukshal, V. / De Bona, P. / Antony, E. / Galletto, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cqk.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cqk.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cq/6cqk ftp://data.pdbj.org/pub/pdb/validation_reports/cq/6cqk | HTTPS FTP |
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-Related structure data
Related structure data | 6cqmC 6cqoSC 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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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 13435.777 Da / Num. of mol.: 4 / Fragment: residues 17-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: RIM1, SCKG_5256, SCKG_5616 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A250WMX0, UniProt: P32445*PLUS |
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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: 2.3 Å3/Da / Density % sol: 46.58 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.2 M MgCl2 and 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97845 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Jan 27, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97845 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→76.57 Å / Num. obs: 12631 / % possible obs: 100 % / Redundancy: 7.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.05 / Net I/σ(I): 12 |
Reflection shell | Resolution: 2.8→2.873 Å / Rmerge(I) obs: 1.967 / Num. measured obs: 18326 / Num. unique obs: 1244 / CC1/2: 0.527 / Rpim(I) all: 0.527 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6CQO Resolution: 2.8→76.57 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.914 / Cross valid method: THROUGHOUT / ESU R: 1.866 / ESU R Free: 0.39 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.62 Å2
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Refinement step | Cycle: 1 / Resolution: 2.8→76.57 Å
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Refine LS restraints |
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