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Yorodumi- PDB-5mem: A potent fluorescent inhibitor of glycogen phosphorylase as a cat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mem | ||||||||||||
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Title | A potent fluorescent inhibitor of glycogen phosphorylase as a catalytic site probe. | ||||||||||||
Components | Glycogen phosphorylase, muscle form | ||||||||||||
Keywords | FLUORESCENT PROTEIN / GP inhibitors / glucopyranosyl cytosine acridine derivatives / electronic absorption spectra / fluorescence spectra | ||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||||||||
Authors | Mamais, M. / Chrysina, E.D. | ||||||||||||
Funding support | Greece, Germany, 3items
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Citation | Journal: Chemistry / Year: 2017 Title: A New Potent Inhibitor of Glycogen Phosphorylase Reveals the Basicity of the Catalytic Site. Authors: Mamais, M. / Degli Esposti, A. / Kouloumoundra, V. / Gustavsson, T. / Monti, F. / Venturini, A. / Chrysina, E.D. / Markovitsi, D. / Gimisis, T. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mem.cif.gz | 177.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mem.ent.gz | 144.9 KB | Display | PDB format |
PDBx/mmJSON format | 5mem.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/5mem ftp://data.pdbj.org/pub/pdb/validation_reports/me/5mem | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: Residue 680 is Lysine (LYS). It appears as LLP since it is covalently bonded with PLP Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MuscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-7LS / |
#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: 2.5 Å3/Da / Density % sol: 50.82 % |
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Crystal grow | Temperature: 289 K / Method: batch mode / pH: 6.8 Details: N,N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid, EDTA, DTT, IMP |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.23953 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.23953 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→86.3 Å / Num. obs: 92031 / % possible obs: 98.9 % / Redundancy: 6.6 % / Biso Wilson estimate: 29.9 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.78→1.88 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.527 / Mean I/σ(I) obs: 4.1 / % possible all: 97.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→86.27 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.307 / SU ML: 0.072 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.1 / 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: 36.08 Å2
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Refinement step | Cycle: 1 / Resolution: 1.78→86.27 Å
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Refine LS restraints |
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