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Yorodumi- PDB-6fd4: Crystal Structure of Human APRT-Tyr105Phe variant in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fd4 | ||||||
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Title | Crystal Structure of Human APRT-Tyr105Phe variant in complex with Adenine, PRPP and Mg2+, 14 hours post crystallization | ||||||
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 / Resolution: 1.5 Å | ||||||
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 | 6fd4.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fd4.ent.gz | 120.8 KB | Display | PDB format |
PDBx/mmJSON format | 6fd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/6fd4 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/6fd4 | HTTPS FTP |
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-Related structure data
Related structure data | 6fchC 6fciC 6fclC 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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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 1 / Auth seq-ID: 3 - 180 / Label seq-ID: 1 - 178
NCS oper:
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-Components
#1: Protein | Mass: 19411.453 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 3-180 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APRT / Plasmid: PET29A / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P07741, adenine phosphoribosyltransferase #2: Chemical | #3: Sugar | #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: 2.28 Å3/Da / Density % sol: 46.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: NAOAC, PEG4000, GLYCEROL, TRIS, PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K PH range: 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→44.64 Å / Num. obs: 51022 / % possible obs: 92.7 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.611 / % possible all: 91.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5HND 5hnd Resolution: 1.5→44.64 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.652 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.076 / ESU R Free: 0.071 / 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: 16.13 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→44.64 Å
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Refine LS restraints |
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