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Yorodumi- PDB-1p2d: Crystal Structure of Glycogen Phosphorylase B in complex with Bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1p2d | |||||||||
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Title | Crystal Structure of Glycogen Phosphorylase B in complex with Beta Cyclodextrin | |||||||||
Components | Glycogen phosphorylase, muscle form | |||||||||
Keywords | TRANSFERASE | |||||||||
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: 1.94 Å | |||||||||
Authors | Pinotsis, N. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G. / Mavridis, I.M. | |||||||||
Citation | Journal: Protein Sci. / Year: 2003 Title: The binding of beta- and gamma-cyclodextrins to glycogen phosphorylase b: Kinetic and crystallographic studies. Authors: Pinotsis, N. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G. / Mavridis, I.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1p2d.cif.gz | 182.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1p2d.ent.gz | 142.5 KB | Display | PDB format |
PDBx/mmJSON format | 1p2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1p2d_validation.pdf.gz | 465.4 KB | Display | wwPDB validaton report |
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Full document | 1p2d_full_validation.pdf.gz | 477.4 KB | Display | |
Data in XML | 1p2d_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | 1p2d_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/1p2d ftp://data.pdbj.org/pub/pdb/validation_reports/p2/1p2d | HTTPS FTP |
-Related structure data
Related structure data | 1p29C 1p2bC 1p2gC 1gfzS 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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Components on special symmetry positions |
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Details | THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. COORDINATES FOR A COMPLETE DIMER REPRESENTING THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE MOLECULE CAN BE GENERATED BY APPLYING THE TWO FOLD AXIS : y,x,1-z |
-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: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose |
#3: Chemical | ChemComp-PLP / |
#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: 2.48 Å3/Da / Density % sol: 50.37 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 / Details: BES, EDTA, pH 6.7, SMALL TUBES, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.7 / Method: unknownDetails: Oikonomakos, N.G., (2000) J.Biol.Chem., 275, 34566. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8068 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 22, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8068 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→30 Å / Num. all: 68504 / Num. obs: 68504 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.076 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.94→1.96 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.499 / % possible all: 85 |
Reflection | *PLUS Lowest resolution: 30 Å / Num. measured all: 714419 / Rmerge(I) obs: 0.076 |
Reflection shell | *PLUS % possible obs: 85 % / Rmerge(I) obs: 0.499 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1GFZ Resolution: 1.94→29.51 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3573624.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 63.2621 Å2 / ksol: 0.380243 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.94→29.51 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.94→2.06 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 30 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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