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Yorodumi- PDB-3bd8: Glucogen Phosphorylase complex with 1(-D-glucopyranosyl) cytosine -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bd8 | |||||||||
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Title | Glucogen Phosphorylase complex with 1(-D-glucopyranosyl) cytosine | |||||||||
Components | Glycogen phosphorylase, muscle form | |||||||||
Keywords | TRANSFERASE / glycogenolysis / type 2 diabetes / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / 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: 2.1 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 | 3bd8.cif.gz | 181.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bd8.ent.gz | 142.4 KB | Display | PDB format |
PDBx/mmJSON format | 3bd8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bd8_validation.pdf.gz | 749.8 KB | Display | wwPDB validaton report |
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Full document | 3bd8_full_validation.pdf.gz | 762.9 KB | Display | |
Data in XML | 3bd8_validation.xml.gz | 33.2 KB | Display | |
Data in CIF | 3bd8_validation.cif.gz | 48 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bd/3bd8 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/3bd8 | HTTPS FTP |
-Related structure data
Related structure data | 3bcrC 3bcsC 3bcuC 3bd6C 3bd7C 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
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Sugar | ChemComp-C3B / |
#4: 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: 0.8113 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 18, 2005 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8113 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 57366 / Num. obs: 57366 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.084 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.49 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2PRJ Resolution: 2.1→29.49 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Refinement step | Cycle: LAST / Resolution: 2.1→29.49 Å
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LS refinement shell | Resolution: 2.1→2.14 Å /
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