[English] 日本語
Yorodumi- PDB-2bfw: Structure of the C domain of glycogen synthase from Pyrococcus abyssi -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bfw | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of the C domain of glycogen synthase from Pyrococcus abyssi | ||||||
Components | GLGA GLYCOGEN SYNTHASE | ||||||
Keywords | TRANSFERASE / GLYCOSYLTRANSFERASE FAMILY 5 UDP/ADP-GLUCOSE-GLYCOGEN SYNTHASE TWO ROSSMAN FOLDS | ||||||
Function / homology | Function and homology information | ||||||
Biological species | PYROCOCCUS ABYSSI (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Horcajada, C. / Guinovart, J.J. / Fita, I. / Ferrer, J.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2006 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2bfw.cif.gz | 59.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2bfw.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 2bfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/2bfw ftp://data.pdbj.org/pub/pdb/validation_reports/bf/2bfw | HTTPS FTP |
---|
-Related structure data
Related structure data | 2bisC 1rzuS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) PYROCOCCUS ABYSSI (archaea) / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring) | ||||
---|---|---|---|---|---|
#2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36.1 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 1.9 |
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 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→42.33 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|