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- PDB-2jga: Crystal structure of human cytosolic 5'-nucleotidase III in compl... -
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Open data
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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 | ||||||
![]() | CYTOSOLIC 5'-NUCLEOTIDASE III | ||||||
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Function / homology | ![]() tRNA 2'-phosphotransferase activity / pyrimidine nucleoside metabolic process / 7-methylguanosine nucleotidase / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 69.1 KB | Display | ![]() |
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PDB format | ![]() | 50.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cn1SC ![]() 2j2cC ![]() 2jc9C ![]() 2jcmC 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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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.) ![]() ![]() ![]() ![]() ![]() ![]() |
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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: ![]() |
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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: ![]() ![]() ![]() |
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![]() |
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 |
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Processing
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Refinement | Method to determine structure![]() ![]() 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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