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Yorodumi- PDB-3qbz: Crystal structure of the Rad53-recognition domain of Saccharomyce... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3qbz | ||||||
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Title | Crystal structure of the Rad53-recognition domain of Saccharomyces cerevisiae Dbf4 | ||||||
Components | DDK kinase regulatory subunit DBF4 | ||||||
Keywords | CELL CYCLE / FHA domain / Rad53 / replication checkpoint | ||||||
Function / homology | Function and homology information positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / premeiotic DNA replication / Activation of the pre-replicative complex ...positive regulation of DNA replication initiation / positive regulation of kinetochore assembly / positive regulation of meiotic DNA double-strand break formation / negative regulation of exit from mitosis / Dbf4-dependent protein kinase complex / positive regulation of meiosis I / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / premeiotic DNA replication / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / mitotic DNA replication checkpoint signaling / DNA replication origin binding / chromosome, centromeric region / DNA replication initiation / protein serine/threonine kinase activator activity / chromosome segregation / positive regulation of protein phosphorylation / cell division / centrosome / chromatin / zinc ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.692 Å | ||||||
Authors | Matthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Saccharomyces cerevisiae Dbf4 has unique fold necessary for interaction with Rad53 kinase. Authors: Matthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A. #1: Journal: Acta Crystallogr.,Sect.F / Year: 2009 Title: Crystallization and preliminary X-ray diffraction analysis of motif N from Saccharomyces cerevisiae Dbf4 Authors: Matthews, L.A. / Duong, A. / Prasad, A.A. / Duncker, B.P. / Guarne, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qbz.cif.gz | 68.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qbz.ent.gz | 50.8 KB | Display | PDB format |
PDBx/mmJSON format | 3qbz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/3qbz ftp://data.pdbj.org/pub/pdb/validation_reports/qb/3qbz | HTTPS FTP |
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-Related structure data
Related structure data | 3oq4S S: Starting model for refinement |
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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: 18993.949 Da / Num. of mol.: 1 / Fragment: residues 66-221, HBRCT domain Source method: isolated from a genetically manipulated source Details: Dbf4 residues 66-221 subcloned in pET15b using NdeI-BamHI Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: D4205, DBF4, DNA52, YD9609.07C, YDR052C / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 STAR pRAREpLysS / References: UniProt: P32325 | ||
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#2: Chemical | #3: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.47 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.9 M ammonium sulfate 50 mM sodium cacodylate 15 mM CYMAL-7, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 10, 2010 / Details: mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→50 Å / Num. obs: 6371 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 53.46 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.042 / Net I/σ(I): 31 |
Reflection shell | Resolution: 2.69→2.74 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.419 / Mean I/σ(I) obs: 3.5 / Num. unique all: 298 / Rsym value: 0.344 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3OQ4 Resolution: 2.692→38.823 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MLHL
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.732 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.692→38.823 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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