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Yorodumi- PDB-7exr: Crystal structure of alkaline alpha-galactosidase D383A mutant fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7exr | |||||||||
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Title | Crystal structure of alkaline alpha-galactosidase D383A mutant from Arabidopsis thaliana complexed with Stachyose. | |||||||||
Components | Probable galactinol--sucrose galactosyltransferase 6 | |||||||||
Keywords | 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 / Probable galactinol--sucrose galactosyltransferase 6 Function and homology information | |||||||||
Biological species | Arabidopsis thaliana (thale cress) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å | |||||||||
Authors | Chuankhayan, P. / Guan, H.H. / Lin, C.C. / Chen, N.C. / Huang, Y.C. / Yoshimura, M. / Nakagawa, A. / Lee, R.H. / Chen, C.J. | |||||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7exr.cif.gz | 306.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7exr.ent.gz | 241.3 KB | Display | PDB format |
PDBx/mmJSON format | 7exr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7exr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7exr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7exr_validation.xml.gz | 57.1 KB | Display | |
Data in CIF | 7exr_validation.cif.gz | 82 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/7exr ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7exr | HTTPS FTP |
-Related structure data
Related structure data | 7exfC 7exgSC 7exhC 7exjC 7exqC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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: 83204.406 Da / Num. of mol.: 2 / Mutation: D383A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: RFS6, DIN10, RS6, At5g20250, F5O24.140 / Production host: Escherichia coli (E. coli) References: UniProt: Q8RX87, galactinol-sucrose galactosyltransferase #2: Polysaccharide | Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.77 Å3/Da / Density % sol: 55.64 % |
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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: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 0.97 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX300HE / Detector: CCD / Date: Mar 28, 2018 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2→30 Å / Num. obs: 124558 / % possible obs: 99.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.04 / Rrim(I) all: 0.101 / Χ2: 1.366 / Net I/σ(I): 7.2 / Num. measured all: 785125 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7EXG Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.689 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.14 / ESU R Free: 0.133 / 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: 155.89 Å2 / Biso mean: 42.678 Å2 / Biso min: 22.5 Å2
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Refinement step | Cycle: final / Resolution: 2→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.003→2.055 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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