+Open data
-Basic information
Entry | Database: PDB / ID: 6fcl | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of Human APRT wild type in complex with AMP | ||||||
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 / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6fcl.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6fcl.ent.gz | 119.2 KB | Display | PDB format |
PDBx/mmJSON format | 6fcl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6fcl_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6fcl_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6fcl_validation.xml.gz | 16.9 KB | Display | |
Data in CIF | 6fcl_validation.cif.gz | 24.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/6fcl ftp://data.pdbj.org/pub/pdb/validation_reports/fc/6fcl | HTTPS FTP |
-Related structure data
Related structure data | 6fchC 6fciC 6fd4C 6fd5C 6fd6C 5ln6 C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19427.453 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: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.64 % |
---|---|
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 |
---|---|
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→44.74 Å / Num. obs: 53495 / % possible obs: 96.2 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 2.6 / % possible all: 94.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LN6 5ln6 Resolution: 1.5→44.74 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.16 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.5 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→44.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|