+Open data
-Basic information
Entry | Database: PDB / ID: 4f9b | ||||||
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Title | Human CDC7 kinase in complex with DBF4 and PHA767491 | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / SER/THR PROTEIN KINASE / TRANSFERASE / PHOSPHORYLATION / CELL CYCLE / CELL DIVISION / MITOSIS / S PHASE / SERINE/THREONINE-PROTEIN KINASE / DBF4-dependent kinase / DDK / ATP-BINDING / NUCLEOTIDE-BINDING / ZINC-BINDING / NUCLEUS / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / enzyme activator activity / Activation of ATR in response to replication stress ...Dbf4-dependent protein kinase complex / regulation of cell cycle phase transition / positive regulation of nuclear cell cycle DNA replication / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / enzyme activator activity / Activation of ATR in response to replication stress / positive regulation of G2/M transition of mitotic cell cycle / protein serine/threonine kinase activator activity / G1/S transition of mitotic cell cycle / mitotic spindle / kinase activity / DNA replication / nucleic acid binding / nuclear body / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / cell division / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / signal transduction / zinc ion binding / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Hughes, S. / Cherepanov, P. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2012 Title: Crystal structure of human CDC7 kinase in complex with its activator DBF4. Authors: Hughes, S. / Elustondo, F. / Di Fonzo, A. / Leroux, F.G. / Wong, A.C. / Snijders, A.P. / Matthews, S.J. / Cherepanov, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4f9b.cif.gz | 179.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f9b.ent.gz | 140.5 KB | Display | PDB format |
PDBx/mmJSON format | 4f9b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/4f9b ftp://data.pdbj.org/pub/pdb/validation_reports/f9/4f9b | HTTPS FTP |
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-Related 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: 40633.828 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CDC7, CDC7L1 / Plasmid: pRSF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2(DE3) References: UniProt: O00311, non-specific serine/threonine protein kinase #2: Protein | Mass: 16923.414 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: coexpression / Source: (gene. exp.) Homo sapiens (human) / Gene: ASK, DBF4, DBF4A, ZDBF1 / Plasmid: pCDF-Duet / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-2(DE3) / References: UniProt: Q9UBU7 #3: Chemical | #4: Chemical | #5: 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: 42.49 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 25% PEG-1500, 15% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 8, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→65.28 Å / Num. all: 35505 / Num. obs: 35150 / % possible obs: 99.9 % / Redundancy: 8.7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.5→2.57 Å / Redundancy: 9 % / Rmerge(I) obs: 0.725 / Mean I/σ(I) obs: 3.1 / Num. unique all: 2533 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→59.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.987 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.478 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.785 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→59.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.566 Å / Total num. of bins used: 20
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