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Yorodumi- PDB-2r4t: Crystal Structure of Wild-type E.coli GS in Complex with ADP and ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2r4t | ||||||
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Title | Crystal Structure of Wild-type E.coli GS in Complex with ADP and Glucose(wtGSc) | ||||||
Components | Glycogen synthase | ||||||
Keywords | TRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP and glucose binding | ||||||
Function / homology | Function and homology information starch synthase (glycosyl-transferring) / alpha-1,4-glucan synthase activity / starch synthase activity / glycogen (starch) synthase activity / glycogen biosynthetic process / DNA damage response / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.258 Å | ||||||
Authors | Sheng, F. / Geiger, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: The crystal structures of the open and catalytically competent closed conformation of Escherichia coli glycogen synthase. Authors: Sheng, F. / Jia, X. / Yep, A. / Preiss, J. / Geiger, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r4t.cif.gz | 124.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r4t.ent.gz | 89.6 KB | Display | PDB format |
PDBx/mmJSON format | 2r4t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/2r4t ftp://data.pdbj.org/pub/pdb/validation_reports/r4/2r4t | HTTPS FTP |
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-Related structure data
Related structure data | 2qzsSC 2r4uC 3copC 3d1jC 3guhC 2qyy S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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
#1: Protein | Mass: 53951.348 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glgA / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A6U8, starch synthase (glycosyl-transferring) |
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#2: Sugar | ChemComp-GLC / |
-Non-polymers , 4 types, 350 molecules
#3: Chemical | ChemComp-ADP / | ||
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#4: Chemical | ChemComp-250 / ( | ||
#5: Chemical | ChemComp-PE3 / #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: 5.7 Å3/Da / Density % sol: 78.3 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.6 Details: 40%(w/v) PEG 4000, 0.2 M Na tartrate and 0.1 M HEPPSO (pH 7.6), VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 24, 2006 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.258→97.13 Å / Num. obs: 56077 / % possible obs: 99.9 % / Observed criterion σ(I): 4.5 / Redundancy: 5.1 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.052 / Χ2: 1.001 / Net I/σ(I): 11.8 |
Reflection shell | Resolution: 2.258→2.34 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 4.5 / Num. unique all: 5555 / Χ2: 0.635 / % possible all: 99.8 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.306 / Cor.coef. Fo:Fc: 0.77
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2QZS Resolution: 2.258→97.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.944 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(I): 4.5 / ESU R: 0.127 / ESU R Free: 0.116 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.998 Å2
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Refinement step | Cycle: LAST / Resolution: 2.258→97.13 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.258→2.317 Å / Total num. of bins used: 20
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