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Yorodumi- PDB-2f3s: Crystal Structure of the glycogen phosphorylase B / ethyl-N-(beta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2f3s | ||||||
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Title | Crystal Structure of the glycogen phosphorylase B / ethyl-N-(beta-D-glucopyranosyl)oxamate complex | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / glycogenolysis / type 2 diabetes | ||||||
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: 1.96 Å | ||||||
Authors | Oikonomakos, N.G. / Leonidas, D.D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2006 Title: Binding of oxalyl derivatives of beta-d-glucopyranosylamine to muscle glycogen phosphorylase b. Authors: Hadjiloi, T. / Tiraidis, C. / Chrysina, E.D. / Leonidas, D.D. / Oikonomakos, N.G. / Tsipos, P. / Gimisis, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2f3s.cif.gz | 181 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2f3s.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 2f3s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2f3s_validation.pdf.gz | 450.9 KB | Display | wwPDB validaton report |
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Full document | 2f3s_full_validation.pdf.gz | 459.5 KB | Display | |
Data in XML | 2f3s_validation.xml.gz | 17.2 KB | Display | |
Data in CIF | 2f3s_validation.cif.gz | 27.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/2f3s ftp://data.pdbj.org/pub/pdb/validation_reports/f3/2f3s | HTTPS FTP |
-Related structure data
Related structure data | 2f3pC 2f3qC 2f3uC 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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Details | Dimeric glycogen phosphorylase is the physiologically active species |
-Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Sugar | ChemComp-7GP / |
#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: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10 mM Bes buffer, 3 mM DDT, 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: 0.8034 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 21, 2005 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8034 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→30 Å / Num. all: 68828 / Num. obs: 68828 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 28.2 Å2 / Rsym value: 0.042 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.96→1.99 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.8 / Num. unique all: 3392 / Rsym value: 0.443 / % possible all: 98.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: pdb entry 2PRj Resolution: 1.96→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.96→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.96→1.99 Å / Rfactor Rfree error: 0.011
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