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Yorodumi- PDB-1udw: Crystal structure of human uridine-cytidine kinase 2 complexed wi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1udw | ||||||
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Title | Crystal structure of human uridine-cytidine kinase 2 complexed with a feedback-inhibitor, CTP | ||||||
Components | Uridine-cytidine kinase 2 | ||||||
Keywords | TRANSFERASE / ALPHA/BETA MONONUCLEOTIDE-BINDING HOLD | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 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 | 1udw.cif.gz | 95.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1udw.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 1udw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1udw_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 1udw_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 1udw_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 1udw_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ud/1udw ftp://data.pdbj.org/pub/pdb/validation_reports/ud/1udw | HTTPS FTP |
-Related 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: 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: 4.02 Å3/Da / Density % sol: 69.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: sodium tartrate, HEPES, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: OXFORD / Detector: CCD / Date: Jan 1, 2002 |
Radiation | Monochromator: rotated-inclined monochromator and vertical focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→39.5 Å / Num. all: 23389 / Num. obs: 23389 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.6→2.69 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.6→39.47 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 274491.49 / 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: 45.8257 Å2 / ksol: 0.371469 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→39.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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