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Yorodumi- PDB-1jdz: CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jdz | ||||||
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Title | CRYSTAL STRUCTURE OF 5'-DEOXY-5'-METHYLTHIOADENOSINE PHOSPHORYLASE WITH FORMYCIN B AND SULFATE ION | ||||||
Components | 5'-METHYLTHIOADENOSINE PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / alpha-beta protein | ||||||
Function / homology | Function and homology information S-methyl-5'-thioadenosine phosphorylase / S-methyl-5-thioadenosine phosphorylase activity / uridine catabolic process / uridine phosphorylase activity / purine-nucleoside phosphorylase / purine nucleoside catabolic process / cytosol Similarity search - Function | ||||||
Biological species | Sulfolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Appleby, T.C. / Mathews, I.I. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2001 Title: Three-dimensional structure of a hyperthermophilic 5'-deoxy-5'-methylthioadenosine phosphorylase from Sulfolobus solfataricus. Authors: Appleby, T.C. / Mathews, I.I. / Porcelli, M. / Cacciapuoti, G. / Ealick, S.E. #1: Journal: J.Biol.Chem. / Year: 1994 Title: Purification and characterization of extremely thermophilic and thermostable 5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. Purine nucleoside phosphorylase ...Title: Purification and characterization of extremely thermophilic and thermostable 5'-methylthioadenosine phosphorylase from the archaeon Sulfolobus solfataricus. Purine nucleoside phosphorylase activity and evidence for intersubunit disulfide bonds Authors: Cacciapuoti, G. / Porcelli, M. / Bertoldo, C. / De Rosa, M. / Zappia, V. #2: Journal: J.Biol.Chem. / Year: 1990 Title: Three-Dimensional Structure of Human Erythrocytic Purine Nucleoside Phosphorylase At 3.2 Resolution Authors: Ealick, S.E. / Rule, S.A. / Carter, D.C. / Greenhough, T.J. / Babu, Y.S. #3: Journal: Structure / Year: 1999 Title: The structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase at 1.7 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 | 1jdz.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jdz.ent.gz | 113.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jdz_validation.pdf.gz | 559.7 KB | Display | wwPDB validaton report |
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Full document | 1jdz_full_validation.pdf.gz | 572.1 KB | Display | |
Data in XML | 1jdz_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 1jdz_validation.cif.gz | 24.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jd/1jdz ftp://data.pdbj.org/pub/pdb/validation_reports/jd/1jdz | HTTPS FTP |
-Related structure data
Related structure data | 1jdsC 1jdtC 1jduC 1jdvC 1je0C 1je1C 1jp7C 1jpvC C: citing same article (ref.) |
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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 | hexamer generated from the trimer in the asymmetric unit by the crystallographic two fold |
-Components
#1: Protein | Mass: 25763.457 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Production host: Escherichia coli (E. coli) References: UniProt: P50389, S-methyl-5'-thioadenosine 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: 2.56 Å3/Da / Density % sol: 51.99 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: dioxane, MPD, MgCl2, NaCl, Tris.HCl, pH 7.4, at VAPOR DIFFUSION, HANGING DROP 291K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Details: used microseeding | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9023 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9023 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 53563 / Num. obs: 53563 / % possible obs: 99.4 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 5.9 |
Reflection shell | Highest resolution: 2 Å / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 2 / % possible all: 97.8 |
Reflection | *PLUS Num. measured all: 261441 |
Reflection shell | *PLUS % possible obs: 97.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: native complex Resolution: 2→20 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 27.1 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Version: 0.9 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5.1 % / Rfactor obs: 0.231 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27.1 Å2 |