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- PDB-7exj: Crystal structure of alkaline alpha-galctosidase D383A mutant fro... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7exj | ||||||
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Title | Crystal structure of alkaline alpha-galctosidase D383A mutant from Arabidopsis thaliana complexed with Raffinose | ||||||
![]() | Probable galactinol--sucrose galactosyltransferase 6 | ||||||
![]() | TRANSFERASE / Alkaline alpha-galactosidase / HYDROLASE | ||||||
Function / homology | galactinol-sucrose galactosyltransferase / galactinol-sucrose galactosyltransferase activity / Glycosyl hydrolases 36 / Raffinose synthase or seed imbibition protein Sip1 / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / raffinose / Probable galactinol--sucrose galactosyltransferase 6![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Chuankhayan, P. / Guan, H.H. / Lin, C.C. / Chen, N.C. / Huang, Y.C. / Yoshimura, M. / Nakagawa, A. / Lee, R.H. / Chen, C.J. | ||||||
![]() | ![]() Title: Structural insight into the hydrolase and synthase activities of an alkaline alpha-galactosidase from Arabidopsis from complexes with substrate/product. Authors: Chuankhayan, P. / Lee, R.H. / Guan, H.H. / Lin, C.C. / Chen, N.C. / Huang, Y.C. / Yoshimura, M. / Nakagawa, A. / Chen, C.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 291.2 KB | Display | ![]() |
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PDB format | ![]() | 231.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 49.7 KB | Display | |
Data in CIF | ![]() | 68.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7exfC ![]() 7exgSC ![]() 7exhC ![]() 7exqC ![]() 7exrC S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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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: 83204.406 Da / Num. of mol.: 2 / Mutation: D383A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: Q8RX87, galactinol-sucrose galactosyltransferase #2: Polysaccharide | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.61 Å3/Da / Density % sol: 52.8 % |
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Crystal grow | Temperature: 291.5 K / Method: microbatch / pH: 7.8 / Details: Tris, PEG 2000, PGA |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.47→30 Å / Num. obs: 118862 / % possible obs: 98.5 % / Redundancy: 3.116 % / Biso Wilson estimate: 67.722 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.061 / Rrim(I) all: 0.074 / Χ2: 1.254 / Net I/σ(I): 10.56 / Num. measured all: 370410 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EXG Resolution: 2.47→30 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.935 / SU B: 12.538 / SU ML: 0.264 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.427 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 167.37 Å2 / Biso mean: 71.143 Å2 / Biso min: 35.44 Å2
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Refinement step | Cycle: final / Resolution: 2.47→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.47→2.534 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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