+Open data
-Basic information
Entry | Database: PDB / ID: 3oq4 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of motif N of Saccharomyces cerevisiae Dbf4 | ||||||
Components | DBF4 | ||||||
Keywords | CELL CYCLE / DDK / BRCT / Rad53 / replication checkpoint / FHA domain / regulatory subunit of DDK / cdc7 / phosphorylation / nuclear | ||||||
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: 2.4 Å | ||||||
Authors | Matthews, L.A. / Jones, D.R. / Prasad, A.A. / Duncker, B.P. / Guarne, A. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of Saccharomyces cerevisiae Dbf4-motif N 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3oq4.cif.gz | 123.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3oq4.ent.gz | 96.7 KB | Display | PDB format |
PDBx/mmJSON format | 3oq4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/3oq4 ftp://data.pdbj.org/pub/pdb/validation_reports/oq/3oq4 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3oq0SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
5 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15622.896 Da / Num. of mol.: 5 / Fragment: residues 120-250 Source method: isolated from a genetically manipulated source Details: Dbf4 residues 120-250 cloned in the multicloning site of 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)STARpRarepLysS / References: UniProt: P32325 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.39 Å3/Da / Density % sol: 63.76 % |
---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1 Details: 22% MPD (v/v) and 100 mM Na/K phosphate buffer pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2009 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. all: 42401 / Num. obs: 42318 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.192 / Rsym value: 0.206 / Net I/σ(I): 8.92 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3OQ0 Resolution: 2.4→46.408 Å / SU ML: 0.27 / σ(F): 1.34 / Phase error: 24.85 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.376 Å2 / ksol: 0.336 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→46.408 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|