+Open data
-Basic information
Entry | Database: PDB / ID: 2no7 | ||||||
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Title | C4S dCK variant of dCK in complex with L-dC+ADP | ||||||
Components | deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / dCK / human deoxycytidine kinase / L-dC / enantiomer / enantioselectivity | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Sabini, E. / Hazra, S. / Konrad, M. / Burley, S.K. / Lavie, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2007 Title: Nonenantioselectivity Property of Human Deoxycytidine Kinase Explained by Structures of the Enzyme in Complex with l- and d-Nucleosides. Authors: Sabini, E. / Hazra, S. / 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 | 2no7.cif.gz | 118.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2no7.ent.gz | 89.9 KB | Display | PDB format |
PDBx/mmJSON format | 2no7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/2no7 ftp://data.pdbj.org/pub/pdb/validation_reports/no/2no7 | HTTPS FTP |
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-Related structure data
Related structure data | 2no0C 2no1C 2no6C 1p5zS S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 32659.588 Da / Num. of mol.: 2 / Mutation: C9S,C45S,C59S,C146S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCK / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / 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: 2.25 Å3/Da / Density % sol: 45.37 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: Reservoir containing 0.95-1.5M trisodium citrate dihydrate and 100mM HEPES, pH 7.5., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 10, 2006 / Details: mirrors |
Radiation | Monochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si (111) sagittal focusing. Rosenbaum-Rock vertical Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 61155 / Num. obs: 57715 / % possible obs: 94.3 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.078 / Net I/σ(I): 15.3 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 3.1 / Num. unique all: 8085 / Rsym value: 0.551 / % possible all: 83.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1P5Z Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.791 / SU ML: 0.091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.124 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.41 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.742 Å / Total num. of bins used: 20
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