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- PDB-2bfw: Structure of the C domain of glycogen synthase from Pyrococcus abyssi -
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Open data
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Basic information
Entry | Database: PDB / ID: 2bfw | ||||||
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Title | Structure of the C domain of glycogen synthase from Pyrococcus abyssi | ||||||
![]() | GLGA GLYCOGEN SYNTHASE | ||||||
![]() | TRANSFERASE / GLYCOSYLTRANSFERASE FAMILY 5 UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE TWO ROSSMAN FOLDS | ||||||
Function / homology | ![]() glycogen (starch) synthase activity / glycogen biosynthetic process / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C. | ||||||
![]() | ![]() Title: Crystal Structure of an Archaeal Glycogen Synthase: Insights Into Oligomerisation and Substrate Binding of Eukaryotic Glycogen Synthases. Authors: Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.2 KB | Display | ![]() |
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PDB format | ![]() | 42.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 448.2 KB | Display | ![]() |
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Full document | ![]() | 449.1 KB | Display | |
Data in XML | ![]() | 11.6 KB | Display | |
Data in CIF | ![]() | 16.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2bisC ![]() 1rzuS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 22251.660 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 218-413 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring) | ||||
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#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36.1 % |
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Crystal grow | pH: 4.6 Details: 30% PEG8K, 0.1 M NAAC PH 4.5, 0.2M LITHIUM SULPHATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEAERCH / Detector: CCD / Date: Nov 12, 2004 / Details: FLAT MIRROR AND A TOROIDAL MIRROR |
Radiation | Monochromator: 2 CRYSTALS MONOCROMATOR. SI(111). 140-X-80 X 20 MM Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→37.9 Å / Num. obs: 15701 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.5 / % possible all: 85.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1RZU Resolution: 1.8→42.33 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.002 / SU ML: 0.098 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.173 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: 15.64 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→42.33 Å
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Refine LS restraints |
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