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Yorodumi- PDB-5hoi: Crystal structure of the carboxy-terminal domain of yeast Ctf4 bo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5hoi | |||||||||
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Title | Crystal structure of the carboxy-terminal domain of yeast Ctf4 bound to Tof2. | |||||||||
Components |
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Keywords | REPLICATION / DNA replication / adaptor protein / beta-propeller domain | |||||||||
Function / homology | Function and homology information negative regulation of septation initiation signaling / establishment of sister chromatid cohesion / protein localization to nucleolar rDNA repeats / Cul8-RING ubiquitin ligase complex / rDNA chromatin condensation / rDNA binding / phosphatase activator activity / rDNA heterochromatin formation / nucleolus organization / double-strand break repair via break-induced replication ...negative regulation of septation initiation signaling / establishment of sister chromatid cohesion / protein localization to nucleolar rDNA repeats / Cul8-RING ubiquitin ligase complex / rDNA chromatin condensation / rDNA binding / phosphatase activator activity / rDNA heterochromatin formation / nucleolus organization / double-strand break repair via break-induced replication / replication fork protection complex / mitotic sister chromatid cohesion / nuclear chromosome / nuclear replication fork / DNA replication initiation / DNA-templated DNA replication / nucleosome assembly / mitotic cell cycle / DNA repair / chromatin binding / nucleolus / mitochondrion / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å | |||||||||
Authors | Simon, A.C. / Pellegrini, L. | |||||||||
Funding support | United Kingdom, 2items
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Citation | Journal: Mol.Cell / Year: 2016 Title: Ctf4 Is a Hub in the Eukaryotic Replisome that Links Multiple CIP-Box Proteins to the CMG Helicase. Authors: Villa, F. / Simon, A.C. / Ortiz Bazan, M.A. / Kilkenny, M.L. / Wirthensohn, D. / Wightman, M. / Matak-Vinkovic, D. / Pellegrini, L. / Labib, K. #1: Journal: Nature / Year: 2014 Title: A Ctf4 trimer couples the CMG helicase to DNA polymerase alpha in the eukaryotic replisome. Authors: Simon, A.C. / Zhou, J.C. / Perera, R.L. / van Deursen, F. / Evrin, C. / Ivanova, M.E. / Kilkenny, M.L. / Renault, L. / Kjaer, S. / Matak-Vinkovic, D. / Labib, K. / Costa, A. / Pellegrini, L. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5hoi.cif.gz | 251.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5hoi.ent.gz | 200.4 KB | Display | PDB format |
PDBx/mmJSON format | 5hoi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ho/5hoi ftp://data.pdbj.org/pub/pdb/validation_reports/ho/5hoi | HTTPS FTP |
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-Related 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: 54447.484 Da / Num. of mol.: 3 / Fragment: UNP residues 472-927 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: CTF4, CHL15, POB1, YPR135W, P9659.7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q01454 #2: Protein/peptide | Mass: 2516.958 Da / Num. of mol.: 3 / Fragment: UNP residues 497-517 / Source method: obtained synthetically Details: The synthetic peptide corresponds to amino acids 497 to 517 of yeast Tof2. Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: Q02208 #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.82 Å3/Da / Density % sol: 56.39 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop Details: 0.2 M tri-sodium citrate pH 6.2, 7-9% PEG 8000 and 0.45-0.9 M NaCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: May 13, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 3.3→48.99 Å / Num. obs: 29749 / % possible obs: 99.3 % / Redundancy: 4.6 % / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.3→3.5 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.1 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Resolution: 3.3→48.99 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.08 / Phase error: 22.64 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.3→48.99 Å
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Refine LS restraints |
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LS refinement shell |
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