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Yorodumi- PDB-1uej: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -
+Open data
-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 | ||||||
Components | Uridine-cytidine kinase 2 | ||||||
Keywords | TRANSFERASE / ALPHA/BETA MONONUCLEOTIDE-BINDING HOLD | ||||||
Function / homology | Function and homology information uridine/cytidine kinase / CTP salvage / uridine kinase activity / Pyrimidine salvage / cytidine kinase activity / UMP salvage / ATP binding / identical protein binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å | ||||||
Authors | Suzuki, N.N. / Koizumi, K. / Fukushima, M. / Matsuda, A. / Inagaki, F. | ||||||
Citation | Journal: STRUCTURE / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uej.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uej.ent.gz | 73.1 KB | Display | PDB format |
PDBx/mmJSON format | 1uej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1uej_validation.pdf.gz | 473.6 KB | Display | wwPDB validaton report |
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Full document | 1uej_full_validation.pdf.gz | 484.9 KB | Display | |
Data in XML | 1uej_validation.xml.gz | 19.2 KB | Display | |
Data in CIF | 1uej_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ue/1uej ftp://data.pdbj.org/pub/pdb/validation_reports/ue/1uej | HTTPS FTP |
-Related structure data
Related structure data | 1udwSC 1ueiC 1ufqC 1uj2C 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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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.) Homo sapiens (human) / Plasmid: pGEX-6P / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9BZX2, uridine/cytidine 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: 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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.9795 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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