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Yorodumi- PDB-5lrf: Crystal structure of Glycogen Phosphorylase b in complex with KS389 -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lrf | ||||||
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Title | Crystal structure of Glycogen Phosphorylase b in complex with KS389 | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / alpha and beta protein | ||||||
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: 1.75 Å | ||||||
Authors | Kantsadi, A.L. / Leonidas, D.D. | ||||||
Citation | Journal: J. Struct. Biol. / Year: 2017 Title: van der Waals interactions govern C-beta-d-glucopyranosyl triazoles' nM inhibitory potency in human liver glycogen phosphorylase. Authors: Kantsadi, A.L. / Stravodimos, G.A. / Kyriakis, E. / Chatzileontiadou, D.S.M. / Solovou, T.G.A. / Kun, S. / Bokor, E. / Somsak, L. / 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 | 5lrf.cif.gz | 179.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lrf.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lrf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lrf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5lrf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5lrf_validation.xml.gz | 32.5 KB | Display | |
Data in CIF | 5lrf_validation.cif.gz | 47.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lr/5lrf ftp://data.pdbj.org/pub/pdb/validation_reports/lr/5lrf | HTTPS FTP |
-Related 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: 97291.203 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 | #3: Chemical | #4: Chemical | ChemComp-PLP / | #5: 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: 2.56 Å3/Da / Density % sol: 51.99 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10mM BES buffer |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.04 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 11, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→38.38 Å / Num. obs: 90698 / % possible obs: 93.2 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.9 / % possible all: 95.5 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→37.14 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.196 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.211 / ESU R Free: 0.194 / 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: 31.502 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→37.14 Å
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Refine LS restraints |
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