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- PDB-1k27: Crystal Structure of 5'-Deoxy-5'-Methylthioadenosine Phosphorylas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k27 | ||||||
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Title | Crystal Structure of 5'-Deoxy-5'-Methylthioadenosine Phosphorylase in Complex with a Transition State Analogue | ||||||
![]() | 5'-Deoxy-5'-Methylthioadenosine Phosphorylase | ||||||
![]() | TRANSFERASE / MTAP / methylthioadenosine phosphorylase / transition state analogue / phosphate | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Shi, W. / Singh, V. / Tyler, P.C. / Furneaux, R.H. / Almo, S.C. / Schramm, V.L. | ||||||
![]() | ![]() Title: Picomolar transition state analogue inhibitors of human 5'-methylthioadenosine phosphorylase and X-ray structure with MT-immucillin-A Authors: Singh, V. / Shi, W. / Evans, G.B. / Tyler, P.C. / Furneaux, R.H. / 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 | ![]() | 69.2 KB | Display | ![]() |
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PDB format | ![]() | 50.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1cg6S S: Starting model for refinement |
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Similar structure data |
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Links
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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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Details | The other two monomers of the biological assembly is generated by the three fold axis, -Y, X-Y, Z; and -X+Y, -X, Z. |
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Components
#1: Protein | Mass: 31277.053 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase |
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#2: Chemical | ChemComp-PO4 / |
#3: Chemical | ChemComp-MTM / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.08 Å3/Da / Density % sol: 60.13 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 6000, Spermidine, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 18 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→20 Å / Num. all: 28021 / Num. obs: 28021 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 7.7 Å2 / Rsym value: 0.064 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 5.8 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2794 / Rsym value: 0.387 / % possible all: 100 |
Reflection | *PLUS Lowest resolution: 20 Å / Num. measured all: 167189 / Rmerge(I) obs: 0.064 |
Reflection shell | *PLUS % possible obs: 100 % / Rmerge(I) obs: 0.386 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1CG6 Resolution: 1.95→20 Å / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: flat model / Bsol: 44.3308 Å2 / ksol: 0.406563 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.95→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
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Refinement | *PLUS Lowest resolution: 20 Å / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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