+Open data
-Basic information
Entry | Database: PDB / ID: 3bcu | ||||||
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Title | Glucogen Phosphorylase complex with thymidine | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / glycogenolysis / type 2 diabetes / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphorylation / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.03 Å | ||||||
Authors | Sovantzis, D.A. / Hadjiloi, T. / Hayes, J.M. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G. | ||||||
Citation | Journal: To be Published Title: D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b Authors: Cisma, C. / Sovantzis, D.A. / Hadjiloi, T. / Stathis, D. / Gimisis, T. / Hayes, J.M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bcu.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bcu.ent.gz | 141.1 KB | Display | PDB format |
PDBx/mmJSON format | 3bcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bc/3bcu ftp://data.pdbj.org/pub/pdb/validation_reports/bc/3bcu | HTTPS FTP |
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-Related structure data
Related structure data | 3bcrC 3bcsC 3bd6C 3bd7C 3bd8C 3bdaC 2prjS 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-THM / |
#3: 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: 2.47 Å3/Da / Density % sol: 50.2 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2005 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. all: 62744 / Num. obs: 62744 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Rsym value: 0.047 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.03→2.06 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.8 / Rsym value: 0.442 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2PRJ Resolution: 2.03→21.59 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.772 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.143 / 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 mean: 36.449 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→21.59 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.031→2.083 Å / Total num. of bins used: 20
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