+Open data
-Basic information
Entry | Database: PDB / ID: 4f99 | ||||||
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Title | Human CDC7 kinase in complex with DBF4 and nucleotide | ||||||
Components |
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Keywords | TRANSFERASE / SER/THR PROTEIN KINASE / PHOSPHORYLATION / CELL CYCLE / CELL DIVISION / MITOSIS / S PHASE / SERINE/THREONINE-PROTEIN KINASE / DBF4-dependent kinase / DDK / ATP-BINDING / NUCLEOTIDE-BINDING / ZINC-BINDING / NUCLEUS | ||||||
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 / mitotic DNA damage checkpoint signaling / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / 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 / mitotic DNA damage checkpoint signaling / cell cycle phase transition / double-strand break repair via break-induced replication / intercellular bridge / Transcriptional Regulation by E2F6 / Activation of the pre-replicative complex / Activation of ATR in response to replication stress / enzyme activator activity / positive regulation of G2/M transition of mitotic cell cycle / protein serine/threonine kinase activator activity / mitotic spindle / G1/S transition of mitotic cell cycle / 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 / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.33 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 | 4f99.cif.gz | 100.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4f99.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 4f99.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4f99_validation.pdf.gz | 764.2 KB | Display | wwPDB validaton report |
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Full document | 4f99_full_validation.pdf.gz | 766.1 KB | Display | |
Data in XML | 4f99_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 4f99_validation.cif.gz | 22.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f9/4f99 ftp://data.pdbj.org/pub/pdb/validation_reports/f9/4f99 | HTTPS FTP |
-Related structure data
Related structure data | 4f9aC 4f9bC 4f9cC 3pvgS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 40633.828 Da / Num. of mol.: 1 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 |
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#2: Protein | Mass: 16923.414 Da / Num. of mol.: 1 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 |
-Non-polymers , 4 types, 51 molecules
#3: Chemical | ChemComp-ADP / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-ZN / |
#6: 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: 1.95 Å3/Da / Density % sol: 36.89 % |
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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: I04 / Wavelength: 0.9763 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2011 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.33→79.14 Å / Num. all: 20628 / Num. obs: 20628 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.33→2.39 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.684 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1470 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PVG (Automatic molecular replacement with BALBES). Resolution: 2.33→59.52 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 6.57 / SU ML: 0.159 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.236 / 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: 42.608 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→59.52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.327→2.388 Å / Total num. of bins used: 20
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