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Yorodumi- PDB-3vue: Crystal Structure of Rice Granule bound Starch Synthase I Catalyt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3vue | ||||||
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Title | Crystal Structure of Rice Granule bound Starch Synthase I Catalytic Domain | ||||||
Components | Granule-bound starch synthase 1, chloroplastic/amyloplastic | ||||||
Keywords | TRANSFERASE / Rossmann fold / glycosyltransferase | ||||||
Function / homology | Function and homology information NDP-glucose-starch glucosyltransferase / ADP-glucose-starch glucosyltransferase activity / starch biosynthetic process / amyloplast / glycogen (starch) synthase activity / IgE binding / chloroplast / ADP binding Similarity search - Function | ||||||
Biological species | Oryza sativa Japonica Group (Japanese rice) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||
Authors | Momma, M. / Fujimoto, Z. | ||||||
Citation | Journal: Biosci.Biotechnol.Biochem. / Year: 2012 Title: Interdomain Disulfide Bridge in the Rice Granule Bound Starch Synthase I Catalytic Domain as Elucidated by X-Ray Structure Analysis Authors: Momma, M. / Fujimoto, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3vue.cif.gz | 110.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3vue.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 3vue.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vu/3vue ftp://data.pdbj.org/pub/pdb/validation_reports/vu/3vue | HTTPS FTP |
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-Related structure data
Related structure data | 3vufC 3guhS 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: 59354.000 Da / Num. of mol.: 1 / Fragment: catalytic domain, UNP residues 83-609 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryza sativa Japonica Group (Japanese rice) Strain: japonica cultivar-group Gene: WAXY, WX, WX-B, Os06g0133000, LOC_Os06g04200, 134P10.7, P0679C08.19 Plasmid: pET45b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3) gold References: UniProt: Q0DEV5, NDP-glucose-starch glucosyltransferase | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 2.51 Å3/Da / Density % sol: 50.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 1.5M Lithium Sulfate, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2009 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 17202 / % possible obs: 99.3 % / Redundancy: 13.5 % / Biso Wilson estimate: 78.6 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 27.5 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 7 / Num. unique all: 1681 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3GUH Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 11.367 / SU ML: 0.235 / Cross valid method: THROUGHOUT / ESU R: 1.792 / ESU R Free: 0.365 / 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 mean: 61.896 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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