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- PDB-3vuf: Crystal Structure of Rice Granule bound Starch Synthase I Catalyt... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3vuf | ||||||
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Title | Crystal Structure of Rice Granule bound Starch Synthase I Catalytic Domain in Complex with ADP | ||||||
![]() | Granule-bound starch synthase 1, chloroplastic/amyloplastic | ||||||
![]() | TRANSFERASE / Rossmann fold / glycosyltransferase | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Momma, M. / Fujimoto, Z. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 111 KB | Display | ![]() |
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PDB format | ![]() | 83.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 702.8 KB | Display | ![]() |
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Full document | ![]() | 717.6 KB | Display | |
Data in XML | ![]() | 20.9 KB | Display | |
Data in CIF | ![]() | 28.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3vueSC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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.) ![]() ![]() Strain: japonica cultivar-group Gene: WAXY, WX, WX-B, Os06g0133000, LOC_Os06g04200, 134P10.7, P0679C08.19 Plasmid: pET45b / Production host: ![]() ![]() References: UniProt: Q0DEV5, NDP-glucose-starch glucosyltransferase | ||
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#2: Chemical | ChemComp-ADP / | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.43 % |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 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: 3→50 Å / Num. obs: 12909 / % possible obs: 99.8 % / Redundancy: 14 % / Biso Wilson estimate: 93.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 24.5 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.669 / Mean I/σ(I) obs: 4.4 / Num. unique all: 1254 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3VUE Resolution: 3→35.19 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 17.379 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R Free: 0.467 / 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: 69.855 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→35.19 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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