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Yorodumi- PDB-5vjn: Crystal Structure of Adenine Phosphoribosyltransferase from Sacch... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5vjn | ||||||
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Title | Crystal Structure of Adenine Phosphoribosyltransferase from Saccharomyces cerevisiae Complexed with D-2,5-Dideoxy-2,5-Imino-Altritol 1,6-Bisphosphate (D-DIAB) and Adenine | ||||||
Components | Adenine phosphoribosyltransferase 1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Adenine phosphoribosyltransferase / Transition state analogue / D-2 / 5-Dideoxy-2 / 5-imino-altritol-1 / 6-bisphosphate / D-DIAB / TRANSFERASE-TRANSFERASE INHIBITOR / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
Function / homology | Function and homology information Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / nucleus ...Purine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / AMP salvage / purine ribonucleoside salvage / AMP binding / Neutrophil degranulation / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Harijan, R.K. / Ducati, R.G. / Bonanno, J.B. / Almo, S.C. / Schramm, V.L. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Synthesis of bis-Phosphate Iminoaltritol Enantiomers and Structural Characterization with Adenine Phosphoribosyltransferase. Authors: Harris, L.D. / Harijan, R.K. / Ducati, R.G. / Evans, G.B. / Hirsch, B.M. / 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 | 5vjn.cif.gz | 91.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5vjn.ent.gz | 67.5 KB | Display | PDB format |
PDBx/mmJSON format | 5vjn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5vjn_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5vjn_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5vjn_validation.xml.gz | 18.8 KB | Display | |
Data in CIF | 5vjn_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vj/5vjn ftp://data.pdbj.org/pub/pdb/validation_reports/vj/5vjn | HTTPS FTP |
-Related structure data
Related structure data | 5vjpC 1g2qS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 3 - 178 / Label seq-ID: 3 - 178
NCS ensembles :
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-Components
#1: Protein | Mass: 20616.814 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Gene: APT1, YML022W / Production host: Escherichia coli (E. coli) References: UniProt: P49435, adenine phosphoribosyltransferase #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-ADE / | #5: 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: 3.05 Å3/Da / Density % sol: 59.66 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 100 mM sodium citrate, pH 5.6, 0.2 M ammonium sulfate, 25% PEG4000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å |
Detector | Type: RAYONIX MX-225HE / Detector: CCD / Date: Feb 9, 2017 |
Radiation | Monochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97931 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→72.85 Å / Num. obs: 46756 / % possible obs: 97.9 % / Redundancy: 3.3 % / Biso Wilson estimate: 18.6 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.78→1.82 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 8584 / CC1/2: 0.53 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1G2Q Resolution: 1.78→72.85 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.834 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.474 Å2
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Refinement step | Cycle: LAST / Resolution: 1.78→72.85 Å
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Refine LS restraints |
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