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Yorodumi- PDB-3l01: Crystal structure of monomeric glycogen synthase from Pyrococcus ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l01 | |||||||||
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Title | Crystal structure of monomeric 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: 2.6 Å | |||||||||
Authors | Diaz, A. / Martinez-Pons, C. / Fita, I. / Ferrer, J.C. / Guinovart, J.J. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: Processivity and Subcellular Localization of Glycogen Synthase Depend on a Non-catalytic High Affinity Glycogen-binding Site. Authors: Diaz, A. / Martinez-Pons, C. / Fita, I. / Ferrer, J.C. / Guinovart, J.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l01.cif.gz | 183.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l01.ent.gz | 144.8 KB | Display | PDB format |
PDBx/mmJSON format | 3l01.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l0/3l01 ftp://data.pdbj.org/pub/pdb/validation_reports/l0/3l01 | HTTPS FTP |
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-Related structure data
Related structure data | 2bisS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Ens-ID: 1 / Refine code: 2
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-Components
-Protein / Sugars , 2 types, 4 molecules AB
#1: Protein | Mass: 48075.199 Da / Num. of mol.: 2 / Fragment: UNP residues 1-426 / Mutation: T426A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pyrococcus abyssi (archaea) / Gene: PYRAB00770, PAB2292 / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3)/pG-Tf2 References: UniProt: Q9V2J8, starch synthase (glycosyl-transferring) #2: Polysaccharide | |
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-Non-polymers , 4 types, 113 molecules
#3: Chemical | ChemComp-K / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.52 Å3/Da / Density % sol: 72.81 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: ammonium sulfate, potassium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.9802 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 7, 2009 / Details: Mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9802 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→25 Å / Num. all: 45476 / Num. obs: 44800 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.095 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.8 / Num. unique all: 6702 / Rsym value: 0.1 / % possible all: 83 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BIS Resolution: 2.6→24.91 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.902 / Occupancy max: 1 / Occupancy min: 1 / SU B: 16.61 / SU ML: 0.164 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.383 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
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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 max: 122.75 Å2 / Biso mean: 38.304 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→24.91 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.6→2.667 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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