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Yorodumi- PDB-2uvq: Crystal structure of human uridine-cytidine kinase 1 in complex w... -
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-Basic information
Entry | Database: PDB / ID: 2uvq | ||||||
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Title | Crystal structure of human uridine-cytidine kinase 1 in complex with ADP | ||||||
Components | URIDINE-CYTIDINE KINASE 1 | ||||||
Keywords | TRANSFERASE / UCK / KINASE / ATP-BINDING / NUCLEOSIDE KINASE / NUCLEOTIDE-BINDING | ||||||
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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E.P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Uppsten, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. | ||||||
Citation | Journal: To be Published Title: Structure of Human Uridine-Cytidine Kinase 1 Authors: Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B. ...Authors: Kosinska, U. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Moche, M. / Nilsson, M.E.P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Uppsten, M. / Thorsell, A.G. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2uvq.cif.gz | 58.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2uvq.ent.gz | 40.8 KB | Display | PDB format |
PDBx/mmJSON format | 2uvq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2uvq_validation.pdf.gz | 734.2 KB | Display | wwPDB validaton report |
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Full document | 2uvq_full_validation.pdf.gz | 736.1 KB | Display | |
Data in XML | 2uvq_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2uvq_validation.cif.gz | 12.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uv/2uvq ftp://data.pdbj.org/pub/pdb/validation_reports/uv/2uvq | HTTPS FTP |
-Related structure data
Related structure data | 2jeoC 1xrjS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28244.295 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-243 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HA47, uridine/cytidine kinase |
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#2: Chemical | ChemComp-ADP / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 53 % |
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Crystal grow | Details: 0.8-1.0 M SUCCINIC ACID PH 6.7-7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 19, 2006 / Details: MIRRORS |
Radiation | Monochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 3→29.4 Å / Num. obs: 12509 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 12.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.7 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.8 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1XRJ Resolution: 3→29.41 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.898 / SU B: 35.166 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.41 Å2
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Refinement step | Cycle: LAST / Resolution: 3→29.41 Å
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Refine LS restraints |
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