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Yorodumi- PDB-6fci: Crystal Structure of Human APRT wild type in complex with Adenine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fci | ||||||
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Title | Crystal Structure of Human APRT wild type in complex with Adenine, 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 / adenine phosphoribosyltransferase activity / grooming behavior / GMP salvage / Purine salvage / IMP salvage / AMP salvage ...Defective APRT disrupts adenine salvage / adenine binding / adenine salvage / adenine phosphoribosyltransferase / adenine phosphoribosyltransferase activity / grooming behavior / GMP salvage / Purine salvage / IMP salvage / AMP salvage / purine ribonucleoside salvage / AMP binding / secretory granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / nucleoplasm / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å | ||||||
Model details | APO | ||||||
Authors | Nioche, P. / Huyet, J. / Ozeir, M. | ||||||
Citation | Journal: Cell Chem Biol / Year: 2018 Title: Structural Insights into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Authors: Huyet, J. / Ozeir, M. / 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: Huyet, J. / Ozeir, M. / 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 | 6fci.cif.gz | 289.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fci.ent.gz | 237.1 KB | Display | PDB format |
PDBx/mmJSON format | 6fci.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fci_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 6fci_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6fci_validation.xml.gz | 32.1 KB | Display | |
Data in CIF | 6fci_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fci ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fci | HTTPS FTP |
-Related structure data
Related structure data | 6fchC 6fclC 6fd4C 6fd5C 6fd6C 5hnd 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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2 |
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Unit cell |
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-Components
#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 / Plasmid: pET29a / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P07741, adenine phosphoribosyltransferase #2: Chemical | ChemComp-MG / #3: Sugar | ChemComp-PRP / #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: 2.22 Å3/Da / Density % sol: 44.48 % |
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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: 0.9762 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 19, 2013 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.94→71.351 Å / Num. all: 45067 / Num. obs: 45067 / % possible obs: 90.9 % / Redundancy: 2.8 % / Rpim(I) all: 0.075 / Rrim(I) all: 0.132 / Rsym value: 0.109 / Net I/av σ(I): 3.982 / Net I/σ(I): 6.7 / Num. measured all: 124409 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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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: 5HND 5hnd Resolution: 1.94→71.35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.871 / SU ML: 0.124 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.23 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 61.5 Å2 / Biso mean: 15.915 Å2 / Biso min: 3.7 Å2
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Refinement step | Cycle: final / Resolution: 1.94→71.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→1.99 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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