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Yorodumi- PDB-2jga: Crystal structure of human cytosolic 5'-nucleotidase III in compl... -
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-Basic information
Entry | Database: PDB / ID: 2jga | ||||||
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Title | Crystal structure of human cytosolic 5'-nucleotidase III in complex with phosphate and magnesium | ||||||
Components | CYTOSOLIC 5'-NUCLEOTIDASE III | ||||||
Keywords | HYDROLASE / PYRIMIDINE 5-PRIME- NUCLEOTIDASE 1 / NUCLEOTIDE METABOLISM / PYRIMIDINE 5-PRIME NUCLEOTIDASE DEFICIENCY / URIDINE 5-PRIME MONOPHOSPHATE HYDROLASE 1 / CYTOSOLIC III / DISEASE MUTATION / NUCLEOTIDE-BINDING / P5N1 / UMPH1 / 5-PRIME / NUCLEOTIDASE | ||||||
Function / homology | Function and homology information tRNA 2'-phosphotransferase activity / pyrimidine nucleoside metabolic process / 7-methylguanosine nucleotidase / Pyrimidine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / defense response to virus / nuclear body ...tRNA 2'-phosphotransferase activity / pyrimidine nucleoside metabolic process / 7-methylguanosine nucleotidase / Pyrimidine catabolism / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / nucleotide metabolic process / defense response to virus / nuclear body / nucleotide binding / magnesium ion binding / endoplasmic reticulum / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. ...Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, M. / Holmberg, B. / Schiavone, L. / Hogbom, M. / Kotenyova, T. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Thorsell, A.G. / Uppenberg, J. / Van Den Berg, S. / Weigelt, J. / Welin, M. / Nordlund, P. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2007 Title: Crystal Structure of Human Cytosolic 5'-Nucleotidase II: Insights Into Allosteric Regulation and Substrate Recognition. Authors: Wallden, K. / Stenmark, P. / Nyman, T. / Flodin, S. / Graslund, S. / Loppnau, P. / Bianchi, V. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2jga.cif.gz | 69.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jga.ent.gz | 50.7 KB | Display | PDB format |
PDBx/mmJSON format | 2jga.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jga_validation.pdf.gz | 439.9 KB | Display | wwPDB validaton report |
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Full document | 2jga_full_validation.pdf.gz | 442.8 KB | Display | |
Data in XML | 2jga_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 2jga_validation.cif.gz | 15.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jg/2jga ftp://data.pdbj.org/pub/pdb/validation_reports/jg/2jga | HTTPS FTP |
-Related structure data
Related structure data | 2cn1SC 2j2cC 2jc9C 2jcmC 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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Unit cell |
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-Components
#1: Protein | Mass: 33227.035 Da / Num. of mol.: 1 / Fragment: RESIDUES 14-286 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9H0P0, 5'-nucleotidase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MG / |
#4: Water | ChemComp-HOH / |
Sequence details | ISOFORM 2 |
-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: 24% PEG1500 AND 20% GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9196 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Apr 22, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9196 Å / Relative weight: 1 |
Reflection | Resolution: 3→77.15 Å / Num. obs: 7057 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 12.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 24.1 |
Reflection shell | Resolution: 3→3.16 Å / Redundancy: 13 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 6.3 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2CN1 Resolution: 3.01→50.19 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.878 / SU B: 37.473 / SU ML: 0.339 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.26 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→50.19 Å
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Refine LS restraints |
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