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Yorodumi- PDB-3guh: Crystal Structure of Wild-type E.coli GS in complex with ADP and DGM -
+Open data
-Basic information
Entry | Database: PDB / ID: 3guh | ||||||
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Title | Crystal Structure of Wild-type E.coli GS in complex with ADP and DGM | ||||||
Components | Glycogen synthase | ||||||
Keywords | TRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / closed-form / ADP and intermediate D-glucopyranosylium binding / Glycogen biosynthesis / Glycosyltransferase | ||||||
Function / homology | Function and homology information starch synthase (glycosyl-transferring) / : / alpha-1,4-glucan glucosyltransferase (ADP-glucose donor) activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) 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: 2.79 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 | 3guh.cif.gz | 117.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3guh.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 3guh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3guh_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 3guh_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3guh_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 3guh_validation.cif.gz | 34.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gu/3guh ftp://data.pdbj.org/pub/pdb/validation_reports/gu/3guh | HTTPS FTP |
-Related structure data
Related structure data | 2qzsC 2r4tC 2r4uC 3copC 3d1jC 1rzuS 2qyy C: citing same article (ref.) S: Starting model for refinement |
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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: b3429, glgA, JW3392 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P0A6U8, starch synthase (glycosyl-transferring) |
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#4: Sugar | ChemComp-ASO / |
-Non-polymers , 5 types, 215 molecules
#2: Chemical | ChemComp-ADP / | ||||
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#3: Chemical | ChemComp-250 / ( | ||||
#5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Details
Nonpolymer details | THE ASO SPECIES IN THIS PDB ENTRY DOES NOT HAVE HYDROGEN ATOM ON C1, THEREFORE IT IS POSITIVELY ...THE ASO SPECIES IN THIS PDB ENTRY DOES NOT HAVE HYDROGEN ATOM ON C1, THEREFORE IT IS POSITIVELY |
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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: 5.62 Å3/Da / Density % sol: 78.13 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.1 Details: 40% (w/v) PEG 4000, 0.2 M NaAc, 0.1 M HEPPSO, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: May 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→97.13 Å / Num. all: 29589 / Num. obs: 29543 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.91 / Redundancy: 8.1 % / Biso Wilson estimate: 62.3 Å2 / Rmerge(I) obs: 0.146 / Χ2: 1.976 / Net I/σ(I): 23.996 |
Reflection shell | Resolution: 2.79→2.9 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.516 / Num. unique all: 2740 / Χ2: 0.511 / % possible all: 92.9 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.349 / Cor.coef. Fo:Fc: 0.744
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RZU Resolution: 2.79→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.184 / WRfactor Rwork: 0.156 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.861 / SU B: 7.902 / SU ML: 0.154 / SU R Cruickshank DPI: 0.287 / SU Rfree: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.287 / ESU R Free: 0.219 / 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 max: 122.93 Å2 / Biso mean: 40.525 Å2 / Biso min: 2 Å2
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Refinement step | Cycle: LAST / Resolution: 2.79→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.79→2.864 Å / Total num. of bins used: 20
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