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Yorodumi- PDB-1p60: Structure of human dCK complexed with 2'-Deoxycytidine and ADP, S... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p60 | ||||||
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Title | Structure of human dCK complexed with 2'-Deoxycytidine and ADP, Space group C 2 2 21 | ||||||
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 / protein homodimerization activity / mitochondrion / nucleoplasm / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.96 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 | 1p60.cif.gz | 118.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p60.ent.gz | 91.1 KB | Display | PDB format |
PDBx/mmJSON format | 1p60.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p60_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 1p60_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 1p60_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 1p60_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/1p60 ftp://data.pdbj.org/pub/pdb/validation_reports/p6/1p60 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 30834.779 Da / Num. of mol.: 2 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 #2: Chemical | #3: Chemical | #4: 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: 2.24 Å3/Da / Density % sol: 44.97 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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 298.0K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 0.9 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Dec 16, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. obs: 39365 / Redundancy: 6.9 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.045 / Net I/σ(I): 23.7 |
Reflection shell | Resolution: 1.96→2 Å / Mean I/σ(I) obs: 3.3 / Rsym value: 0.291 |
Reflection | *PLUS Num. obs: 39237 / % possible obs: 97.4 % / Num. measured all: 270973 / Rmerge(I) obs: 0.045 |
Reflection shell | *PLUS Lowest resolution: 2 Å / % possible obs: 67.8 % / Rmerge(I) obs: 0.291 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.96→30 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.09 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / 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: 26.099 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.965→2.016 Å / Total num. of bins used: 20 /
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Refinement | *PLUS Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.203 / Rfactor Rwork: 0.161 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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