[English] 日本語
Yorodumi- PDB-3s0j: The crystal structure of glycogen phosphorylase b in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s0j | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The crystal structure of glycogen phosphorylase b in complex with 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-chlorobenzene | |||||||||
Components | Glycogen phosphorylase, muscle form | |||||||||
Keywords | TRANSFERASE / glycogenolysis | |||||||||
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 Å | |||||||||
Authors | Alexacou, K.-M. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G. / Leonidas, D.D. | |||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2011 Title: Halogen-substituted (C-beta-D-glucopyranosyl)-hydroquinone regioisomers: synthesis, enzymatic evaluation and their binding to glycogen phosphorylase. Authors: Alexacou, K.M. / Zhang, Y.Z. / Praly, J.P. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G. / Leonidas, D.D. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3s0j.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3s0j.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 3s0j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s0/3s0j ftp://data.pdbj.org/pub/pdb/validation_reports/s0/3s0j | HTTPS FTP |
---|
-Related structure data
Related structure data | 3np7C 3np9C 3npaC 2prjS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Sugar | ChemComp-Z15 / ( |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.02 % |
---|---|
Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10 mM BES Buffer, 3 mM DTT, 1 mM IMP, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8156 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 27, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8156 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 65452 / Num. obs: 64845 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 31.1 Å2 / Rsym value: 0.065 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 5.2 / Num. unique all: 3213 / Rsym value: 0.398 / % possible all: 90.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2PRJ Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.957 / SU B: 3.703 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 35.178 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
|