+Open data
-Basic information
Entry | Database: PDB / ID: 4mra | ||||||
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Title | Crystal structure of Gpb in complex with QUERCETIN | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | Transferase/transferase inhibitor / alpha and beta protein / Transferase-transferase inhibitor complex | ||||||
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: 2.34 Å | ||||||
Authors | Kantsadi, L.A. / Chatzileontiadou, S.M.D. / Leonidas, D.D. | ||||||
Citation | Journal: Food Chem.Toxicol. / Year: 2014 Title: Biochemical and biological assessment of the inhibitory potency of extracts from vinification byproducts of Vitis vinifera extracts against glycogen phosphorylase. Authors: Kantsadi, A.L. / Apostolou, A. / Theofanous, S. / Stravodimos, G.A. / Kyriakis, E. / Gorgogietas, V.A. / Chatzileontiadou, D.S. / Pegiou, K. / Skamnaki, V.T. / Stagos, D. / Kouretas, D. / ...Authors: Kantsadi, A.L. / Apostolou, A. / Theofanous, S. / Stravodimos, G.A. / Kyriakis, E. / Gorgogietas, V.A. / Chatzileontiadou, D.S. / Pegiou, K. / Skamnaki, V.T. / Stagos, D. / Kouretas, D. / Psarra, A.M. / Haroutounian, S.A. / Leonidas, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4mra.cif.gz | 186.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4mra.ent.gz | 143.7 KB | Display | PDB format |
PDBx/mmJSON format | 4mra.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mr/4mra ftp://data.pdbj.org/pub/pdb/validation_reports/mr/4mra | HTTPS FTP |
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-Related structure data
Related structure data | 3symS 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: 95509.031 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-QUE / |
#3: Chemical | ChemComp-DMS / |
#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: 50.29 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10mM BES buffer, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 23, 2013 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→30 Å / Num. all: 40399 / Num. obs: 40399 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Rsym value: 0.101 / Net I/σ(I): 18 |
Reflection shell | Resolution: 2.34→2.38 Å / Redundancy: 10 % / Mean I/σ(I) obs: 5 / Rsym value: 0.461 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 3SYM Resolution: 2.34→29.23 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.901 / SU B: 7.084 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.348 / ESU R Free: 0.248 / 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: 30.332 Å2
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Refinement step | Cycle: LAST / Resolution: 2.34→29.23 Å
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Refine LS restraints |
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