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- PDB-2ske: PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHITE, GLUCOSE AND ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2ske | |||||||||
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Title | PYRIDOXAL PHOSPHORYLASE B IN COMPLEX WITH PHOSPHITE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE | |||||||||
![]() | PYRIDOXAL PHOSPHORYLASE B | |||||||||
![]() | TRANSFERASE / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / ALLOSTERIC ENZYME / PYRIDOXAL PHOSPHATE | |||||||||
Function / homology | ![]() 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 | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Oikonomakos, N.G. / Zographos, S.E. / Tsitsanou, K.E. / Johnson, L.N. / Acharya, K.R. | |||||||||
![]() | ![]() Title: Activator anion binding site in pyridoxal phosphorylase b: the binding of phosphite, phosphate, and fluorophosphate in the crystal. Authors: Oikonomakos, N.G. / Zographos, S.E. / Tsitsanou, K.E. / Johnson, L.N. / Acharya, K.R. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 186.4 KB | Display | ![]() |
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PDB format | ![]() | 145.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2skcC ![]() 2skdC ![]() 2prjS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
-Protein / Sugars , 2 types, 2 molecules A![](data/chem/img/GLC.gif)
![](data/chem/img/GLC.gif)
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: IN COMPLEX WITH PHOSPHITE, GLUCOSE AND INOSINE-5'-MONOPHOSPHATE Source: (natural) ![]() ![]() |
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#2: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 265 molecules ![](data/chem/img/PO3.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PLP.gif)
![](data/chem/img/IMP.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-PO3 / |
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#4: Chemical | ChemComp-PLP / |
#5: Chemical | ChemComp-IMP / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.7 Details: T-STATE PYRIDOXAL PHOSPHORYLASE B, FROM RABBIT MUSCLE, WAS CO-CRYSTALLIZED WITH 8-10 MM FLUOROPHOSPHATE IN A MEDIUM CONSISTING OF 15-25 MG/ML ENZYME, 2 MM IMP, 2 MM SPERMINE, 50 MM GLUCOSE, ...Details: T-STATE PYRIDOXAL PHOSPHORYLASE B, FROM RABBIT MUSCLE, WAS CO-CRYSTALLIZED WITH 8-10 MM FLUOROPHOSPHATE IN A MEDIUM CONSISTING OF 15-25 MG/ML ENZYME, 2 MM IMP, 2 MM SPERMINE, 50 MM GLUCOSE, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (16 DEGREE C). JUST BEFORE DATA COLLECTION, THE CRYSTALS WERE TRANSFERRED TO A FRESH BUFFER SOLUTION, CONTAINING THE SAME CONSTITUENTS AS THEIR MOTHER LIQUOR WITH THE EXCEPTION OF THE PROTEIN., VAPOR DIFFUSION, HANGING DROP, temperature 289K | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions |
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Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Detector: FILM / Date: Oct 21, 1993 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.46→16.88 Å / Num. all: 30529 / Num. obs: 30529 / % possible obs: 84.89 % / Observed criterion σ(I): 0 / Redundancy: 3.039 % / Rmerge(I) obs: 0.074 |
Reflection shell | Resolution: 2.46→2.57 Å / % possible all: 65 |
Reflection | *PLUS Num. measured all: 98321 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PRJ Resolution: 2.46→16.88 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.46→16.88 Å
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Refine LS restraints |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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