+Open data
-Basic information
Entry | Database: PDB / ID: 3d1j | ||||||
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Title | Crystal Structure of E.coli GS mutant dmGS(C7S;C408S) | ||||||
Components | Glycogen synthase | ||||||
Keywords | TRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / open form / Glycogen biosynthesis / Glycosyltransferase | ||||||
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: 3 Å | ||||||
Authors | Sheng, F. / Geiger, J.H. | ||||||
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 | 3d1j.cif.gz | 104 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3d1j.ent.gz | 79.4 KB | Display | PDB format |
PDBx/mmJSON format | 3d1j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d1/3d1j ftp://data.pdbj.org/pub/pdb/validation_reports/d1/3d1j | HTTPS FTP |
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-Related structure data
Related structure data | 2qzsC 2r4tC 2r4uC 3copC 3guhC 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
#1: Protein | Mass: 52848.078 Da / Num. of mol.: 1 / Mutation: C7S, C408S 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: 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: 4.23 Å3/Da / Density % sol: 70.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 40% (w/v) PEG 4000, 0.1 M Tris, 0.2 M Na tartrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 98 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 16, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. all: 21907 / Num. obs: 20539 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 63.9 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 28.3 |
Reflection shell | Resolution: 3→3.15 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2 / Num. unique all: 2180 / % possible all: 100 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.54 / Cor.coef. Fo:Fc: 0.485
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1RZU Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.903 / SU B: 14.38 / SU ML: 0.266 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.909 / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 50.651 Å2
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Refinement step | Cycle: LAST / Resolution: 3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.078 Å / Total num. of bins used: 20
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