+Open data
-Basic information
Entry | Database: PDB / ID: 2a0w | |||||||||
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Title | Structure of human purine nucleoside phosphorylase H257G mutant | |||||||||
Components | Purine nucleoside phosphorylase | |||||||||
Keywords | TRANSFERASE / purine nucleoside phosphorylase / transition state inhibitor / mutant | |||||||||
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 / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / 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 / response to xenobiotic stimulus / immune response / Neutrophil degranulation / extracellular exosome / extracellular region / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.28 Å | |||||||||
Authors | Murkin, A.S. / Shi, W. / Schramm, V.L. | |||||||||
Citation | Journal: Biochemistry / Year: 2007 Title: Neighboring group participation in the transition state of human purine nucleoside phosphorylase. Authors: Murkin, A.S. / Birck, M.R. / Rinaldo-Matthis, A. / Shi, W. / Taylor, E.A. / 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 | 2a0w.cif.gz | 71.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a0w.ent.gz | 51.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a0w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a0/2a0w ftp://data.pdbj.org/pub/pdb/validation_reports/a0/2a0w | HTTPS FTP |
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-Related structure data
Related structure data | 2a0xC 2a0yC 2oc4C 2oc9C 2on6C 1rszS C: citing same article (ref.) 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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Details | The biological assembly is a trimer generated from the monomer in the asymmetric unit by the crystallographic 3-fold |
-Components
#1: Protein | Mass: 32103.783 Da / Num. of mol.: 1 / Mutation: H257G Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: NP, PNP / Production host: Escherichia coli (E. coli) References: UniProt: P00491, purine-nucleoside phosphorylase | ||||
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#2: Chemical | #3: Chemical | ChemComp-DIH / | #4: 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: 4.7 Å3/Da / Density % sol: 76 % |
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Crystal grow | Temperature: 291 K / pH: 5.6 Details: Na citrate, ammonium sulfate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 5.60 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 14, 2004 |
Radiation | Monochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 2.28→50 Å / Num. obs: 29413 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 35.3 Å2 / Rsym value: 0.046 / Net I/σ(I): 50.2 |
Reflection shell | Resolution: 2.28→2.36 Å / Mean I/σ(I) obs: 8.3 / Rsym value: 0.196 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 1RSZ Resolution: 2.28→50 Å / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: ENGH & HUBER
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Displacement parameters | Biso mean: 46 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.28→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.28→2.42 Å / Rfactor Rfree error: 0.013
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