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Yorodumi- PDB-1cg6: STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1cg6 | ||||||
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Title | STRUCTURE OF HUMAN 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE AT 1.7 A RESOLUTION | ||||||
Components | PROTEIN (5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE) | ||||||
Keywords | TRANSFERASE / METHYLTHIOADENOSINE PHOSPHORYLASE / PURINE NUCLEOSIDE PHOSPHORYLASE / PURINE SALVAGE / METHYLTHIOADENOSINE / SULFATE | ||||||
Function / homology | Function and homology information 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 / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / 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 / purine ribonucleoside salvage / nucleobase-containing compound metabolic process / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å | ||||||
Authors | Appleby, T.C. / Erion, M.D. / Ealick, S.E. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 A resolution provides insights into substrate binding and catalysis. Authors: Appleby, T.C. / Erion, M.D. / Ealick, S.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1cg6.cif.gz | 67.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1cg6.ent.gz | 49.5 KB | Display | PDB format |
PDBx/mmJSON format | 1cg6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cg/1cg6 ftp://data.pdbj.org/pub/pdb/validation_reports/cg/1cg6 | 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: 31277.053 Da / Num. of mol.: 1 / Mutation: ILE56VAL Source method: isolated from a genetically manipulated source Details: COMPLEXED WITH 5'-DEOXY-5'-METHYLTHIOADENOSINE AND SULFATE Source: (gene. exp.) Homo sapiens (human) / Tissue: PLACENTA Description: MTAP CDNA WAS ISOLATED FROM A HUMAN PLACENTA CDNA LIBRARY AND EXPRESSED IN E. COLI Cellular location: CYTOPLASM / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q13126, S-methyl-5'-thioadenosine phosphorylase |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-MTA / |
#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: 3 Å3/Da / Density % sol: 59 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.4 Details: 12% (W/V) PEG 6000, 25% (V/V) ETHYLENE GLYCOL, 0.2M TRIS-HCL PH 7.8, 0.002M DTT, pH 7.4 | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.919 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 15, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.919 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 42292 / % possible obs: 96.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.5 Å2 / Rsym value: 5.3 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6 % / Mean I/σ(I) obs: 6.5 / Rsym value: 10.6 / % possible all: 93.2 |
Reflection | *PLUS Num. measured all: 393633 / Rmerge(I) obs: 0.053 |
Reflection shell | *PLUS % possible obs: 93.2 % / Rmerge(I) obs: 0.106 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.7→8 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 21.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10.1 % / Rfactor obs: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 21.2 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.299 / % reflection Rfree: 9.6 % / Rfactor Rwork: 0.287 |