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Yorodumi- PDB-1rzu: Crystal structure of the glycogen synthase from A. tumefaciens in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rzu | ||||||
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Title | Crystal structure of the glycogen synthase from A. tumefaciens in complex with ADP | ||||||
Components | Glycogen synthase 1 | ||||||
Keywords | TRANSFERASE / glycosyl-transferase / GT-B fold / Rossmann fold / ADP-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 / cytosol Similarity search - Function | ||||||
Biological species | Agrobacterium tumefaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Buschiazzo, A. / Guerin, M.E. / Ugalde, J.E. / Ugalde, R.A. / Shepard, W. / Alzari, P.M. | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation. Authors: Buschiazzo, A. / Ugalde, J.E. / Guerin, M.E. / Shepard, W. / Ugalde, R.A. / Alzari, P.M. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2003 Title: Preliminary crystallographic studies of glycogen synthase from Agrobacterium tumefaciens Authors: Guerin, M.E. / Buschiazzo, A. / Ugalde, J.E. / Ugalde, R.A. / Alzari, P.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rzu.cif.gz | 193.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rzu.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 1rzu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/1rzu ftp://data.pdbj.org/pub/pdb/validation_reports/rz/1rzu | 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
#1: Protein | Mass: 52456.793 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: GLGA1, GLGA, ATU4075, AGR_L_1562 / Plasmid: pET22 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P0A3F3, starch synthase (glycosyl-transferring) #2: Chemical | #3: 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: 2.5 Å3/Da / Density % sol: 50.5 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, isopropanol, HEPES, ADP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9393 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 2, 2003 Details: channel - cut Si monochromator + cylindrical grazing incidence mirror |
Radiation | Monochromator: channel cut Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 40385 / Num. obs: 40385 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 42.18 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.062 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 2.9 / Num. unique all: 5557 / Rsym value: 0.062 / % possible all: 85.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Non complexed form of glycogen synthase (Agrobacterium tumefaciens) Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU ML: 267.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.483 / ESU R Free: 0.25 / Stereochemistry target values: Engh & Huber Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, TLS refinemente has been performed
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.453 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.36 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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