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Yorodumi- PDB-2xsq: Crystal structure of human Nudix motif 16 (NUDT16) in complex wit... -
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-Basic information
Entry | Database: PDB / ID: 2xsq | ||||||
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Title | Crystal structure of human Nudix motif 16 (NUDT16) in complex with IMP and magnesium | ||||||
Components | U8 SNORNA-DECAPPING ENZYME | ||||||
Keywords | HYDROLASE / MRNA DECAPPING / MRNA TURNOVER / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing ...inosine diphosphate phosphatase / sno(s)RNA catabolic process / dIDP phosphatase activity / dITP catabolic process / IDP phosphatase activity / positive regulation of cell cycle process / RNA NAD-cap (NMN-forming) hydrolase activity / phosphodiesterase decapping endonuclease activity / dITP diphosphatase activity / negative regulation of rRNA processing / NAD-cap decapping / 5'-(N7-methylguanosine 5'-triphospho)-[mRNA] hydrolase / 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity / Phosphate bond hydrolysis by NUDT proteins / metalloexopeptidase activity / cobalt ion binding / chloride ion binding / snoRNA binding / mRNA catabolic process / manganese ion binding / nucleotide binding / mRNA binding / nucleolus / magnesium ion binding / protein homodimerization activity / nucleoplasm / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å | ||||||
Authors | Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. ...Tresaugues, L. / Welin, M. / Arrowsmith, C.H. / Berglund, H. / Bountra, C. / Collins, R. / Edwards, A.M. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Johansson, I. / Karlberg, T. / Kol, S. / Kotenyova, T. / Kouznetsova, E. / Moche, M. / Nyman, T. / Persson, C. / Schuler, H. / Schutz, P. / Siponen, M.I. / Thorsell, A.G. / van den Berg, S. / Wahlberg, E. / Weigelt, J. / Nordlund, P. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Structural Basis for the Specificity of Human Nudt16 and its Regulation by Inosine Monophosphate. Authors: Tresaugues, L. / Lundback, T. / Welin, M. / Flodin, S. / Nyman, T. / Silvander, C. / Graslund, S. / Nordlund, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xsq.cif.gz | 59 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xsq.ent.gz | 41.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xs/2xsq ftp://data.pdbj.org/pub/pdb/validation_reports/xs/2xsq | HTTPS FTP |
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-Related structure data
Related structure data | 3couS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23889.180 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: MAMMALIAN GENE COLLECTION (MGC) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)R3 PRARE References: UniProt: Q96DE0, Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides | ||||
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#2: Chemical | ChemComp-IMP / | ||||
#3: Chemical | #4: Chemical | ChemComp-CL / | #5: 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: 2.48 Å3/Da / Density % sol: 50.41 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: PROTEIN WAS MIXED WITH 5MM MGCL2 AND 2MM IDP PRIOR SETTING-UP THE PLATES. THEN IT WAS CRYSTALLIZED FROM 20MM MGCL2, 22% W/V POLYACRYLIC ACID 5100 AND 0.1M HEPES PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9792 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 8, 2010 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→42.69 Å / Num. obs: 25010 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 21.062 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.72→1.81 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 1.1 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3COU Resolution: 1.72→81.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.627 / SU ML: 0.053 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.085 / 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: 15.756 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.72→81.74 Å
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