+Open data
-Basic information
Entry | Database: PDB / ID: 2p0e | ||||||
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Title | Human nicotinamide riboside kinase 1 in complex with tiazofurin | ||||||
Components | Nicotinamide riboside kinase 1 | ||||||
Keywords | TRANSFERASE / non-protein kinase / NAD+ / nicotinamide riboside / nrk1 / tiazofurin / ADP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC | ||||||
Function / homology | Function and homology information nicotinate riboside kinase / ribosylnicotinate kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / phosphorylation / ATP binding / metal ion binding ...nicotinate riboside kinase / ribosylnicotinate kinase activity / ribosylnicotinamide kinase / ribosylnicotinamide kinase activity / Nicotinate metabolism / NAD metabolic process / NAD biosynthetic process / phosphorylation / ATP binding / metal ion binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å | ||||||
Authors | Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Brenner, C. ...Rabeh, W.M. / Tempel, W. / Nedyalkova, L. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Brenner, C. / Park, H. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: Plos Biol. / Year: 2007 Title: Nicotinamide Riboside Kinase Structures Reveal New Pathways to NAD(+). Authors: Tempel, W. / Rabeh, W.M. / Bogan, K.L. / Belenky, P. / Wojcik, M. / Seidle, H.F. / Nedyalkova, L. / Yang, T. / Sauve, A.A. / Park, H.W. / Brenner, C. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN. THE BIOLOGICAL UNIT ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2p0e.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2p0e.ent.gz | 42.5 KB | Display | PDB format |
PDBx/mmJSON format | 2p0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p0/2p0e ftp://data.pdbj.org/pub/pdb/validation_reports/p0/2p0e | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | not known |
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 24373.371 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NRK1, C9orf95 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codon plus RIL References: UniProt: Q9NWW6, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor |
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-Non-polymers , 5 types, 170 molecules
#2: Chemical | ChemComp-PO4 / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-TIZ / ( |
#5: Chemical | ChemComp-UNX / |
#6: 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: 2.5 Å3/Da / Density % sol: 50.85 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 9 Details: 20% PEG 3350, 0.2M Sodium phosphate monobasic, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Feb 6, 2007 | |||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→20 Å / Num. obs: 43446 / % possible obs: 98.9 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11 | |||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: same protein in complex with nicotinamide mononucleotide based on an isomorphous crystal Resolution: 1.8→19.838 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.185 / SU ML: 0.07 / ESU R: 0.112 / ESU R Free: 0.11 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Molprobity, prodrg, coot programs have also been used in the refinement
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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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.171 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→19.838 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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