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Yorodumi- PDB-3v91: Structure of T82M glycogenin mutant truncated at residue 270 comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3v91 | ||||||
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Title | Structure of T82M glycogenin mutant truncated at residue 270 complexed with UDP-glucose | ||||||
Components | Glycogenin-1 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / UDP-alpha-D-glucose:glucosyl-glycogenin alpha-D-glucosyltransferase activity / glycogen biosynthetic process / manganese ion binding / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å | ||||||
Authors | Carrizo, M.E. / Romero, J.M. / Issoglio, F.M. / Curtino, J.A. | ||||||
Citation | Journal: Febs Lett. / Year: 2012 Title: Structural and biochemical insight into glycogenin inactivation by the glycogenosis-causing T82M mutation. Authors: Carrizo, M.E. / Romero, J.M. / Issoglio, F.M. / Curtino, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3v91.cif.gz | 70.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3v91.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 3v91.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v9/3v91 ftp://data.pdbj.org/pub/pdb/validation_reports/v9/3v91 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 32637.760 Da / Num. of mol.: 1 / Fragment: UNP residues 1-271 / Mutation: T82M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: GYG, GYG1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: P13280, glycogenin glucosyltransferase |
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-Non-polymers , 5 types, 97 molecules
#2: Chemical | ChemComp-GOL / |
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#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-MN / |
#5: Chemical | ChemComp-UPG / |
#6: 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: 2.77 Å3/Da / Density % sol: 55.53 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 12% PEGMME5000/0.2M ammonium sulfate/sodium MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.43 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 17, 2010 / Details: Mirrors |
Radiation | Monochromator: Silicium curved crystal, with asymmetric 7.25 angle cut Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.43 Å / Relative weight: 1 |
Reflection | Resolution: 2→25.37 Å / Num. all: 24729 / Num. obs: 24729 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.308 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3579 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2→25.37 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 3.288 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.147 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2→25.37 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.002→2.054 Å / Total num. of bins used: 20
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