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Yorodumi- PDB-2jc9: Crystal structure of Human Cytosolic 5'-Nucleotidase II in comple... -
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-Basic information
Entry | Database: PDB / ID: 2jc9 | ||||||
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Title | Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with adenosine | ||||||
Components | CYTOSOLIC PURINE 5'-NUCLEOTIDASE | ||||||
Keywords | HYDROLASE / CYTOSOLIC 5-PRIME NUCLEOTIDASE II / GMP-IMP SPECIFIC NUCLEOTIDASE / CN-II / NT5C2 / POLYMORPHISM / CYTOSOLIC PURINE 5-PRIME NUCLEOTIDASE / ALLOSTERIC ENZYME / HIGH KM 5-PRIME NUCLEOTIDASE | ||||||
Function / homology | Function and homology information nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity ...nucleoside phosphotransferase / nucleoside phosphotransferase activity / dGMP metabolic process / GMP metabolic process / Abacavir metabolism / negative regulation of defense response to virus by host / GMP 5'-nucleotidase activity / adenosine metabolic process / IMP-specific 5'-nucleotidase / IMP 5'-nucleotidase activity / IMP metabolic process / Ribavirin ADME / IMP catabolic process / Purine catabolism / allantoin metabolic process / XMP 5'-nucleosidase activity / 5'-nucleotidase / 5'-nucleotidase activity / protein K48-linked ubiquitination / ubiquitin protein ligase activity / ATP binding / metal ion binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. ...Wallden, K. / Stenmark, P. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ehn, M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg, S.L. / Hogbom, M. / Karlberg, T. / Kotenyova, T. / Magnusdottir, A. / Nilsson-Ehle, P. / Nyman, T. / Ogg, D. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Thorsell, A.G. / Van Den Berg, S. / Loppnau, P. / 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 | 2jc9.cif.gz | 230.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2jc9.ent.gz | 181.9 KB | Display | PDB format |
PDBx/mmJSON format | 2jc9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jc9 ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jc9 | HTTPS FTP |
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-Related structure data
Related structure data | 2cn1C 2j2cSC 2jcmC 2jgaC 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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 64088.930 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-536 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: P28A-LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE) / References: UniProt: P49902, 5'-nucleotidase |
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-Non-polymers , 5 types, 504 molecules
#2: Chemical | #3: Chemical | ChemComp-MG / | #4: Chemical | ChemComp-SO4 / #5: Chemical | #6: 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: 3.16 Å3/Da / Density % sol: 61.13 % |
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Crystal grow | pH: 8.5 / Details: 1.8 M MAGNESIUM SULFATE, 0.1 M TRIS PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93926 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 8, 2006 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93926 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→74.95 Å / Num. obs: 122218 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J2C Resolution: 1.5→74.33 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.961 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / 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: 16.18 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→74.33 Å
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