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Yorodumi- PDB-1bx3: EFFECTS OF COMMONLY USED CRYOPROTECTANTS ON GLYCOGEN PHOSPHORYLAS... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1bx3 | ||||||
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Title | EFFECTS OF COMMONLY USED CRYOPROTECTANTS ON GLYCOGEN PHOSPHORYLASE ACTIVITY AND STRUCTURE | ||||||
Components | PROTEIN (GLYCOGEN PHOSPHORYLASE B) | ||||||
Keywords | TRANSFERASE / PHOSPHORYLASE / INHIBITOR / CRYOPROTECTANT / MPD / DMSO / CRYOCRYSTALLOGRAPHY | ||||||
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 / OTHER / Resolution: 2.3 Å | ||||||
Authors | Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W.J. | ||||||
Citation | Journal: Protein Sci. / Year: 1999 Title: Effects of commonly used cryoprotectants on glycogen phosphorylase activity and structure. Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W. #1: Journal: Glycogen Phosphorylase B: Description of the Protein Structure Year: 1991 Title: Glycogen Phosphorylase B: Description of the Protein Structure Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1bx3.cif.gz | 188.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1bx3.ent.gz | 147.4 KB | Display | PDB format |
PDBx/mmJSON format | 1bx3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/1bx3 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/1bx3 | HTTPS FTP |
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-Related structure data
Related structure data | 1b4dC 2gpnS S: Starting model for refinement C: citing same article (ref.) |
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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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-Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: SCHIFF'S BASE LINK BETWEEN PLP AND LYS 680 / Source: (natural) Oryctolagus cuniculus (rabbit) / Cellular location: CYTOPLASM / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: 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: 2.35 Å3/Da / Density % sol: 47.66 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / pH: 6.7 Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M EDTA, 0.02 % (W/V) SODIUM AZIDE AT 16 DEGREES C. THE CRYSTALS WERE CRYOPROTECTED WITH 30% (V/V) ...Details: THE PROTEIN WAS CRYSTALLIZED FROM 0.01 M BES, PH 6.7, 0.003 M DTT, 0.001 M SPERMINE, 0.0001 M EDTA, 0.02 % (W/V) SODIUM AZIDE AT 16 DEGREES C. THE CRYSTALS WERE CRYOPROTECTED WITH 30% (V/V) DMSO (DIMETHYLSULFOXIDE)., temperature 289K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknownDetails: Oikonomakos, N.G., (1985) Biochim.Biophys.Acta., 832, 248. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.928 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→36.8 Å / Num. obs: 41713 / % possible obs: 99.9 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 20.59 |
Reflection shell | Resolution: 2.3→2.34 Å / Rmerge(I) obs: 0.103 / Mean I/σ(I) obs: 10.48 / % possible all: 99.5 |
Reflection | *PLUS Num. measured all: 244996 |
Reflection shell | *PLUS % possible obs: 99.5 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER Starting model: PDB ENTRY 2GPN Resolution: 2.3→36.8 Å / Cross valid method: FREE R-FACTOR / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→36.8 Å
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Refine LS restraints |
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