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Yorodumi- PDB-5ikp: Crystal structure of human brain glycogen phosphorylase bound to AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ikp | ||||||
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Title | Crystal structure of human brain glycogen phosphorylase bound to AMP | ||||||
Components | Glycogen phosphorylase, brain form | ||||||
Keywords | TRANSFERASE / GP / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / GLYCOGEN DISEASE / GLYCOSYLTRANSFERASE / NUCLEOTIDE-BINDING / ALLOSTERIC ENZYME | ||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / azurophil granule lumen / pyridoxal phosphate binding / Neutrophil degranulation / extracellular exosome ...glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / azurophil granule lumen / pyridoxal phosphate binding / Neutrophil degranulation / extracellular exosome / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Mathieu, C. / Li de la Sierra-Gallay, I. / Xu, X. / Haouz, A. / Rodrigues-Lima, F. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2016 Title: Insights into Brain Glycogen Metabolism: THE STRUCTURE OF HUMAN BRAIN GLYCOGEN PHOSPHORYLASE. Authors: Mathieu, C. / de la Sierra-Gallay, I.L. / Duval, R. / Xu, X. / Cocaign, A. / Leger, T. / Woffendin, G. / Camadro, J.M. / Etchebest, C. / Haouz, A. / Dupret, J.M. / Rodrigues-Lima, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5ikp.cif.gz | 178.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ikp.ent.gz | 138.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ikp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ikp_validation.pdf.gz | 745.1 KB | Display | wwPDB validaton report |
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Full document | 5ikp_full_validation.pdf.gz | 753.3 KB | Display | |
Data in XML | 5ikp_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 5ikp_validation.cif.gz | 39 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ik/5ikp ftp://data.pdbj.org/pub/pdb/validation_reports/ik/5ikp | HTTPS FTP |
-Related structure data
Related structure data | 5ikoC 1z8dS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 97110.203 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PYGB / Production host: Escherichia coli (E. coli) / References: UniProt: P11216, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-AMP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.71 Å3/Da / Density % sol: 54.63 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 28 % (v/v) PEG 400, 0.2 M calcium chloride, and 0.1 M HEPES, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 16, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8729 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→47.56 Å / Num. obs: 15352 / % possible obs: 99.7 % / Redundancy: 19 % / Net I/σ(I): 27.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1Z8D Resolution: 3.4→47.56 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.897 / SU B: 37.541 / SU ML: 0.559 / Cross valid method: THROUGHOUT / ESU R Free: 0.685 / 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: 119.289 Å2
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Refinement step | Cycle: 1 / Resolution: 3.4→47.56 Å
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Refine LS restraints |
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