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- PDB-1uej: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1uej | ||||||
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Title | Crystal structure of human uridine-cytidine kinase 2 complexed with a substrate, cytidine | ||||||
![]() | Uridine-cytidine kinase 2 | ||||||
![]() | TRANSFERASE / ALPHA/BETA MONONUCLEOTIDE-BINDING HOLD | ||||||
Function / homology | ![]() uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding ...uridine/cytidine kinase / CTP salvage / ribosylnicotinamide kinase activity / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / phosphorylation / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F. | ||||||
![]() | ![]() Title: Structural basis for the specificity, catalysis, and regulation of human uridine-cytidine kinase Authors: Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003 Title: Crystallization and preliminary X-ray analysis of human uridine-cytidine kinase 2 Authors: Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 96.5 KB | Display | ![]() |
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PDB format | ![]() | 73.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.6 KB | Display | ![]() |
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Full document | ![]() | 484.9 KB | Display | |
Data in XML | ![]() | 19.2 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1udwSC ![]() 1ueiC ![]() 1ufqC ![]() 1uj2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 28262.994 Da / Num. of mol.: 2 / Fragment: residues 1-250 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.11 Å3/Da / Density % sol: 69.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: sodium citrate, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 10, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 23533 / Num. obs: 23533 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.27 / Num. unique all: 2358 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1UDW Resolution: 2.61→37.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 982277.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 42.4696 Å2 / ksol: 0.374115 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 48.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.61→37.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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