[English] 日本語
Yorodumi- PDB-2jcm: Crystal structure of Human Cytosolic 5'-Nucleotidase II in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2jcm | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Human Cytosolic 5'-Nucleotidase II in complex with beryllium trifluoride | ||||||
Components | CYTOSOLIC PURINE 5'-NUCLEOTIDASE | ||||||
Keywords | HYDROLASE / CYTOSOLIC 5-PRIME NUCLEOTIDASE II / GMP-IMP SPECIFIC NUCLEOTIDASE / CN-II / NT5C2 / 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 / Ribavirin ADME / IMP metabolic process / 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 / identical protein binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 Schiavone, 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2jcm.cif.gz | 119.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2jcm.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 2jcm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2jcm_validation.pdf.gz | 444.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2jcm_full_validation.pdf.gz | 450.7 KB | Display | |
Data in XML | 2jcm_validation.xml.gz | 21.3 KB | Display | |
Data in CIF | 2jcm_validation.cif.gz | 31.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/2jcm ftp://data.pdbj.org/pub/pdb/validation_reports/jc/2jcm | HTTPS FTP |
-Related structure data
Related structure data | 2cn1C 2j2cSC 2jc9C 2jgaC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 64153.930 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 | ||
---|---|---|---|
#2: Chemical | ChemComp-UNX / | ||
#3: Chemical | ChemComp-MG / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.13 % |
---|---|
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 |
---|---|
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: 2.15→20 Å / Num. obs: 41406 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 7.14 |
Reflection shell | Resolution: 2.15→2.2 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.36 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2J2C Resolution: 2.15→20.67 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.891 / SU B: 11.496 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 13.27 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→20.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|