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- PDB-3ozd: Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphoryl... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3ozd | ||||||
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Title | Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA | ||||||
![]() | S-methyl-5'-thioadenosine phosphorylase | ||||||
![]() | TRANSFERASE / 5'-methylthioadenosine / phosphorylase / MTAP / pCl-phenylthioDADMeImmA | ||||||
Function / homology | ![]() Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation ...Methionine salvage pathway / S-methyl-5'-thioadenosine phosphorylase / 1,4-alpha-oligoglucan phosphorylase activity / S-methyl-5-thioadenosine phosphorylase activity / L-methionine salvage from methylthioadenosine / nucleobase-containing compound metabolic process / purine ribonucleoside salvage / response to testosterone / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / methylation / extracellular exosome / nucleoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Ho, M. / Guan, R. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() Title: Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase Authors: Ho, M. / Guan, R. / Almo, S.C. / Schramm, V.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 115.4 KB | Display | ![]() |
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PDB format | ![]() | 94.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 976.7 KB | Display | ![]() |
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Full document | ![]() | 985.6 KB | Display | |
Data in XML | ![]() | 23.7 KB | Display | |
Data in CIF | ![]() | 32.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 31277.053 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.83 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2M NaCl, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Detector: CCD / Date: Mar 10, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0809 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.1→20 Å / Num. obs: 42831 / % possible obs: 99.5 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.124 / Χ2: 1.014 / Net I/σ(I): 6.6 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 66.65 Å2 / Biso mean: 35.7552 Å2 / Biso min: 3.48 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.152 Å / Total num. of bins used: 20
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