+Open data
-Basic information
Entry | Database: PDB / ID: 5msm | ||||||||||||
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Title | Structure of the Dcc1-Ctf8-Ctf18C Trimer | ||||||||||||
Components |
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Keywords | CELL CYCLE / winged-helix / DNA repair | ||||||||||||
Function / homology | Function and homology information maintenance of mitotic sister chromatid cohesion / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / nuclear replication fork / chromosome, centromeric region / DNA replication initiation / double-strand break repair via homologous recombination / DNA replication / chromatin ...maintenance of mitotic sister chromatid cohesion / Ctf18 RFC-like complex / maintenance of DNA trinucleotide repeats / mitotic sister chromatid cohesion / nuclear replication fork / chromosome, centromeric region / DNA replication initiation / double-strand break repair via homologous recombination / DNA replication / chromatin / ATP hydrolysis activity / mitochondrion / DNA binding / ATP binding / nucleus Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae S288c (yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | ||||||||||||
Authors | Wade, B.O. / Singleton, M.R. | ||||||||||||
Funding support | United Kingdom, 3items
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Citation | Journal: EMBO Rep. / Year: 2017 Title: Structural studies of RFC(C)(tf18) reveal a novel chromatin recruitment role for Dcc1. Authors: Wade, B.O. / Liu, H.W. / Samora, C.P. / Uhlmann, F. / Singleton, M.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5msm.cif.gz | 226.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5msm.ent.gz | 181 KB | Display | PDB format |
PDBx/mmJSON format | 5msm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ms/5msm ftp://data.pdbj.org/pub/pdb/validation_reports/ms/5msm | HTTPS FTP |
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-Related structure data
Related structure data | 5msnSC 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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Unit cell |
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-Components
#1: Protein | Mass: 44133.785 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: DCC1, YCL016C, YCL16C / Production host: Escherichia coli (E. coli) / References: UniProt: P25559 #2: Protein | Mass: 15189.688 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CTF8, YHR191C / Production host: Escherichia coli (E. coli) / References: UniProt: P38877 #3: Protein | Mass: 8915.728 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Gene: CTF18, CHL12, YMR078C, YM9582.03C / Production host: Escherichia coli (E. coli) / References: UniProt: P49956 #4: 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: 2.14 Å3/Da / Density % sol: 42.47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Bis-Tris Propane pH 6.3, 0.2M NaBr and 17% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 26, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→60.64 Å / Num. obs: 46232 / % possible obs: 90 % / Redundancy: 3 % / Rmerge(I) obs: 0.08522 / Net I/σ(I): 7.15 |
Reflection shell | Resolution: 2.29→2.372 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.4557 / Mean I/σ(I) obs: 1.31 / Num. unique all: 2926 / % possible all: 57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5MSN Resolution: 2.29→60.64 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.12
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.29→60.64 Å
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Refine LS restraints |
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LS refinement shell |
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