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Yorodumi- PDB-6hgq: Crystal Structure of Human APRT wild type in complex with Hypoxan... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hgq | ||||||
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Title | Crystal Structure of Human APRT wild type in complex with Hypoxanthine, PRPP and Mg2+ | ||||||
Components | Adenine phosphoribosyltransferase | ||||||
Keywords | TRANSFERASE / Rossman fold | ||||||
Function / homology | Function and homology information Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / GMP salvage / grooming behavior / IMP salvage / Purine salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase activity / adenine phosphoribosyltransferase / GMP salvage / grooming behavior / IMP salvage / Purine salvage / AMP salvage / purine ribonucleoside salvage / AMP binding / secretory granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 Å | ||||||
Model details | APO | ||||||
Authors | Nioche, P. / Huyet, J. / Ozeir, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural basis for substrate selectivity and nucleophilic substitution mechanisms in human adenine phosphoribosyltransferase catalyzed reaction. Authors: Ozeir, M. / Huyet, J. / Burgevin, M.C. / Pinson, B. / Chesney, F. / Remy, J.M. / Siddiqi, A.R. / Lupoli, R. / Pinon, G. / Saint-Marc, C. / Gibert, J.F. / Morales, R. / Ceballos-Picot, I. / ...Authors: Ozeir, M. / Huyet, J. / Burgevin, M.C. / Pinson, B. / Chesney, F. / Remy, J.M. / Siddiqi, A.R. / Lupoli, R. / Pinon, G. / Saint-Marc, C. / Gibert, J.F. / Morales, R. / Ceballos-Picot, I. / Barouki, R. / Daignan-Fornier, B. / Olivier-Bandini, A. / Auge, F. / Nioche, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hgq.cif.gz | 292.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hgq.ent.gz | 238.9 KB | Display | PDB format |
PDBx/mmJSON format | 6hgq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hgq ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hgq | HTTPS FTP |
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-Related structure data
Related structure data | 6hgpC 6hgrC 6hgsC 6fchS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein / Sugars , 2 types, 8 molecules ACDB
#1: Protein | Mass: 19498.531 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: protein bought from Euromedex, cat# ATGP0483 / Source: (gene. exp.) Homo sapiens (human) / Gene: APRT / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P07741, adenine phosphoribosyltransferase #4: Sugar | ChemComp-PRP / |
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-Non-polymers , 4 types, 354 molecules
#2: Chemical | ChemComp-GOL / | ||||
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#3: Chemical | ChemComp-MG / #5: Chemical | ChemComp-HPA / #6: 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: 2.19 Å3/Da / Density % sol: 43.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: NaOAc, PEG4000, Glycerol, Tris |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.966 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→71.69 Å / Num. all: 47031 / Num. obs: 47031 / % possible obs: 90 % / Redundancy: 2.4 % / Rpim(I) all: 0.054 / Rrim(I) all: 0.092 / Rsym value: 0.073 / Net I/av σ(I): 6.098 / Net I/σ(I): 8.6 / Num. measured all: 112869 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FCH Resolution: 1.9→71.69 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.478 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1925 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.193 / ESU R Free: 0.158 / 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 max: 69.71 Å2 / Biso mean: 22.045 Å2 / Biso min: 6.61 Å2
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Refinement step | Cycle: final / Resolution: 1.9→71.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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