+Open data
-Basic information
Entry | Database: PDB / ID: 2jcs | ||||||
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Title | Active site mutant of dNK from D. melanogaster with dTTP bound | ||||||
Components | DEOXYNUCLEOSIDE KINASE | ||||||
Keywords | TRANSFERASE / KINASE / ATP-BINDING / DNA SYNTHESIS / NUCLEOTIDE- BINDING / DEOXYRIBONUCLEOSIDE KINASE | ||||||
Function / homology | Function and homology information deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity ...deoxynucleoside kinase / Pyrimidine salvage / deoxynucleoside kinase activity / nucleoside salvage / uridine kinase activity / deoxycytidine kinase activity / nucleoside phosphate biosynthetic process / thymidine kinase activity / deoxyguanosine kinase activity / deoxyadenosine kinase activity / cytidine kinase activity / DNA biosynthetic process / kinase activity / phosphorylation / mitochondrion / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | DROSOPHILA MELANOGASTER (fruit fly) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Egeblad-Welin, L. / Sonntag, Y. / Eklund, H. / Munch-Petersen, B. | ||||||
Citation | Journal: FEBS J. / Year: 2007 Title: Functional Studies of Active-Site Mutants from Drosophila Melanogaster Deoxyribonucleoside Kinase. Investigations of the Putative Catalytic Glutamate- Arginine Pair and of Residues Responsible ...Title: Functional Studies of Active-Site Mutants from Drosophila Melanogaster Deoxyribonucleoside Kinase. Investigations of the Putative Catalytic Glutamate- Arginine Pair and of Residues Responsible for Substrate Specificity. Authors: Egeblad-Welin, L. / Sonntag, Y. / Eklund, H. / Munch-Petersen, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jcs.cif.gz | 100.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jcs.ent.gz | 75.2 KB | Display | PDB format |
PDBx/mmJSON format | 2jcs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jcs ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jcs | HTTPS FTP |
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-Related structure data
Related structure data | 1oe0S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 1
NCS oper: (Code: given Matrix: (-1, 0.001845, 0.003595), Vector: |
-Components
#1: Protein | Mass: 26892.682 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-230 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9XZT6, deoxynucleoside kinase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | |
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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: 2.82 Å3/Da / Density % sol: 55.98 % |
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Crystal grow | pH: 6.5 / Details: 0.12 M NAAC,0.1 M MES PH 6.5, 18% MPEG 2000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.087 |
Detector | Type: MARRESEARCH / Detector: CCD / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.087 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→32.28 Å / Num. obs: 18797 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OE0 Resolution: 2.5→32.28 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.474 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.564 / ESU R Free: 0.273 / 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: 37.14 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→32.28 Å
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Refine LS restraints |
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