+Open data
-Basic information
Entry | Database: PDB / ID: 2zi5 | ||||||
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Title | C4S dCK variant of dCK in complex with L-dA+UDP | ||||||
Components | Deoxycytidine kinase | ||||||
Keywords | TRANSFERASE / dCK / purine / deoxyadenosine / deoxycytidine kinase / nucleoside / enantiomer / L-dA / UDP / ATP-binding / Nucleotide-binding / Nucleus / Phosphoprotein | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.77 Å | ||||||
Authors | Sabini, E. / Lavie, A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structural basis for substrate promiscuity of dCK Authors: Sabini, E. / Hazra, S. / 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 | 2zi5.cif.gz | 206.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zi5.ent.gz | 161.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zi5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zi5_validation.pdf.gz | 2.8 MB | Display | wwPDB validaton report |
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Full document | 2zi5_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 2zi5_validation.xml.gz | 42.1 KB | Display | |
Data in CIF | 2zi5_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zi/2zi5 ftp://data.pdbj.org/pub/pdb/validation_reports/zi/2zi5 | HTTPS FTP |
-Related structure data
Related structure data | 2zi3C 2zi4C 2zi6C 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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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 32572.510 Da / Num. of mol.: 4 / Mutation: C9S, C45S, C59S, C146S 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 | ChemComp-UDP / #3: Chemical | ChemComp-3L1 / ( #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: 2.19 Å3/Da / Density % sol: 43.84 % |
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0M Sodium Citrate, 100mM Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 7, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.77→30 Å / Num. all: 110589 / Num. obs: 110589 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 16.6 |
Reflection shell | Resolution: 1.77→1.87 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 3.1 / Num. unique all: 17048 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1P5Z Resolution: 1.77→30 Å / σ(F): 0 / σ(I): 0
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Refinement step | Cycle: LAST / Resolution: 1.77→30 Å
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Refine LS restraints |
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