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Yorodumi- PDB-4ear: Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ear | ||||||
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Title | Crystal structure of purine nucleoside phosphorylase (W16Y, W94Y, W178Y, H257W) mutant from human complexed with DADMe-ImmG and phosphate | ||||||
Components | Purine nucleoside phosphorylase | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / PNP / Immucillin / Purine nucleoside phosphorylase / nucleoside binding / purine base binding / purine-nucleoside phosphorylase activity / drug binding / transferase activity / transferring glycosyl groups / phosphate ion binding / cytosol / 6-FLUORO-L-TRYPTOPHAN / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / nucleotide biosynthetic process / urate biosynthetic process ...nicotinamide riboside catabolic process / Defective PNP disrupts phosphorolysis of (deoxy)guanosine and (deoxy)inosine / purine-containing compound salvage / deoxyinosine catabolic process / purine nucleobase binding / inosine catabolic process / deoxyadenosine catabolic process / dAMP catabolic process / nucleotide biosynthetic process / urate biosynthetic process / Ribavirin ADME / IMP catabolic process / nucleoside binding / guanosine phosphorylase activity / Purine catabolism / allantoin metabolic process / Purine salvage / purine-nucleoside phosphorylase / purine-nucleoside phosphorylase activity / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / positive regulation of alpha-beta T cell differentiation / phosphate ion binding / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / secretory granule lumen / ficolin-1-rich granule lumen / immune response / response to xenobiotic stimulus / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Haapalainen, A.M. / Ho, M.C. / Suarez, J.J. / Almo, S.C. / Schramm, V.L. | ||||||
Citation | Journal: Chem.Biol. / Year: 2013 Title: Catalytic Site Conformations in Human PNP by (19)F-NMR and Crystallography. Authors: Suarez, J. / Haapalainen, A.M. / Cahill, S.M. / Ho, M.C. / Yan, F. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ear.cif.gz | 191.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ear.ent.gz | 157.3 KB | Display | PDB format |
PDBx/mmJSON format | 4ear.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/4ear ftp://data.pdbj.org/pub/pdb/validation_reports/ea/4ear | 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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-Components
#1: Protein | Mass: 36145.117 Da / Num. of mol.: 3 / Mutation: W16Y, W94Y, W178Y, H257W Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP, X00737.1 / Plasmid: pCRT7/NT-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: P00491, purine-nucleoside phosphorylase #2: Chemical | #3: Chemical | #4: 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: 2.33 Å3/Da / Density % sol: 47.14 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% PEG 1000, 0.1M Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2011 Details: Rosenbaum-Rock double crystal sagittal focusing monochrometer and vertical focusing mirror |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→50 Å / Num. all: 113686 / Num. obs: 110270 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 47.3 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 8 % / Rmerge(I) obs: 0.914 / Mean I/σ(I) obs: 2.6 / Num. unique all: 5375 / Rsym value: 0.914 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→41.24 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 2.954 / SU ML: 0.087 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.094 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.67 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→41.24 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.744 Å / Total num. of bins used: 20
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