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Yorodumi- PDB-3s28: The crystal structure of sucrose synthase-1 in complex with a bre... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3s28 | |||||||||
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Title | The crystal structure of sucrose synthase-1 in complex with a breakdown product of the UDP-glucose | |||||||||
Components | Sucrose synthase 1 | |||||||||
Keywords | TRANSFERASE / Glycosyltransferase / Sucrose metabolism / sugar donar complex / Rossmann fold / GT-B fold / Glycosyltansferase / UDP-glucose / cytosol | |||||||||
Function / homology | Function and homology information sucrose synthase / response to flooding / sucrose synthase activity / response to mannitol / response to sorbitol / sucrose metabolic process / response to sucrose / response to water deprivation / plasmodesma / response to osmotic stress ...sucrose synthase / response to flooding / sucrose synthase activity / response to mannitol / response to sorbitol / sucrose metabolic process / response to sucrose / response to water deprivation / plasmodesma / response to osmotic stress / response to glucose / response to cold / cellular response to hypoxia / response to hypoxia / cytosol Similarity search - Function | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Zheng, Y. / Garavito, R.M. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2011 Title: The Structure of Sucrose Synthase-1 from Arabidopsis thaliana and Its Functional Implications. Authors: Zheng, Y. / Anderson, S. / Zhang, Y. / Garavito, R.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3s28.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb3s28.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 3s28.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3s28_validation.pdf.gz | 3.1 MB | Display | wwPDB validaton report |
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Full document | 3s28_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 3s28_validation.xml.gz | 237.6 KB | Display | |
Data in CIF | 3s28_validation.cif.gz | 313.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s2/3s28 ftp://data.pdbj.org/pub/pdb/validation_reports/s2/3s28 | HTTPS FTP |
-Related structure data
Related structure data | 3s27SC 3s29C 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 94178.617 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: col / Gene: At5g20830, SUS1, T1M15.230 / Plasmid: pET17 / Production host: Escherichia coli (E. coli) / Strain (production host): Rossetta(DE3) / References: UniProt: P49040, sucrose synthase |
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-Sugars , 2 types, 16 molecules
#3: Sugar | ChemComp-LCN / #4: Sugar | ChemComp-NHF / |
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-Non-polymers , 5 types, 490 molecules
#2: Chemical | ChemComp-UDP / #5: Chemical | ChemComp-SO4 / #6: Chemical | ChemComp-MLA / #7: Chemical | ChemComp-K / #8: 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: 3.65 Å3/Da / Density % sol: 66.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 1.85-1.90 M AMMONIUM SULFATE, 80-100 MM SODIUM CITRATE pH 6.1, 0.15 M SODIUM POTASSIUM TARTRATE, 150 mM SUCROSE, 5 mM URIDINE DIPHOSPHATE GLUCOSE, vapor diffusion, sitting drop, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 7, 2010 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→185.269 Å / Num. all: 263585 / Num. obs: 263585 / % possible obs: 99.7 % / Redundancy: 3 % / Rsym value: 0.114 / Net I/σ(I): 9.1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3S27 Resolution: 2.8→24.976 Å / Occupancy max: 1 / Occupancy min: 0.14 / FOM work R set: 0.8349 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 24.2 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.04 Å2 / ksol: 0.328 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 174.61 Å2 / Biso mean: 47.6281 Å2 / Biso min: 13.31 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→24.976 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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