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Yorodumi- PDB-1p61: Structure of human dCK complexed with 2'-Deoxycytidine and ADP, P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p61 | ||||||
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Title | Structure of human dCK complexed with 2'-Deoxycytidine and ADP, P 43 21 2 space group | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / nucleoside kinase / P-loop / deoxycytidine | ||||||
Function / homology | Function and homology information deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity ...deoxycytidine kinase / 2'-deoxyadenosine kinase / deoxyguanosine kinase / dAMP salvage / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / deoxyguanosine kinase activity / deoxyadenosine kinase activity / Pyrimidine salvage / cytidine kinase activity / pyrimidine nucleotide metabolic process / Purine salvage / phosphorylation / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.21 Å | ||||||
Authors | Sabini, E. / Ort, S. / Monnerjahn, C. / Konrad, M. / Lavie, A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2003 Title: Structure of human dCK suggests strategies to improve anticancer and antiviral therapy Authors: Sabini, E. / Ort, S. / Monnerjahn, C. / Konrad, M. / Lavie, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p61.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p61.ent.gz | 47.4 KB | Display | PDB format |
PDBx/mmJSON format | 1p61.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p61 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p61 | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 30834.779 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P27707, deoxycytidine kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Chemical | ChemComp-DCZ / |
#4: 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: 2.44 Å3/Da / Density % sol: 49.52 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.95-1.0M citrate trisodium dihydrate, 100mM Hepes, 5mM deoxycytidine, 5mM ADP, 5mM MgCl2, 5mM DTT, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9552 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 21, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9552 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 15208 / Rsym value: 0.064 / Net I/σ(I): 28.2 |
Reflection shell | Resolution: 2.2→2.3 Å / Mean I/σ(I) obs: 7.5 / Rsym value: 0.156 |
Reflection | *PLUS Num. obs: 15406 / % possible obs: 95.9 % / Num. measured all: 219344 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 78.2 % / Rmerge(I) obs: 0.156 |
-Processing
Software | Name: REFMAC / Version: 5.1.24 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MAD / Resolution: 2.21→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.278 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.314 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.706 Å2
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Refinement step | Cycle: LAST / Resolution: 2.21→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.209→2.266 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Highest resolution: 2.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.221 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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