+Open data
-Basic information
Entry | Database: PDB / ID: 3qen | ||||||
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Title | S74E dCK in complex with 5-bromodeoxycytidine and UDP | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / alpha/beta / phosphoryl transfer / phosphorylation | ||||||
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: 1.997 Å | ||||||
Authors | Lavie, A. / Hazra, S. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Post-translational phosphorylation of serine 74 of human deoxycytidine kinase favors the enzyme adopting the open conformation making it competent for nucleoside binding and release. Authors: Hazra, S. / Szewczak, A. / Ort, 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 | 3qen.cif.gz | 115.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qen.ent.gz | 88.2 KB | Display | PDB format |
PDBx/mmJSON format | 3qen.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qe/3qen ftp://data.pdbj.org/pub/pdb/validation_reports/qe/3qen | HTTPS FTP |
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-Related structure data
Related structure data | 3qejC 3qeoC 1p5zS 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
#1: Protein | Mass: 32614.549 Da / Num. of mol.: 2 / Mutation: S74E,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) / Strain (production host): C41 / 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: 2.18 Å3/Da / Density % sol: 43.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 7.5 Details: 12 mg/ml protein mixed with 0.9-1.5M trisodium citrate di-hydrate and 100 mM Tris, pH 7.5, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 93 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 | |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.997→69.171 Å / Num. all: 37828 / Num. obs: 37632 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.061 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P5Z Resolution: 1.997→69.171 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.1 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.042 / ESU R Free: 0.038 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.915 Å2
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Refinement step | Cycle: LAST / Resolution: 1.997→69.171 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.997→2.049 Å / Total num. of bins used: 20
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