+Open data
-Basic information
Entry | Database: PDB / ID: 3axh | |||||||||
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Title | Crystal structure of isomaltase in complex with isomaltose | |||||||||
Components | Oligo-1,6-glucosidase IMA1 | |||||||||
Keywords | HYDROLASE / (BETA/ALPHA)8-BARREL | |||||||||
Function / homology | Function and homology information disaccharide catabolic process / oligo-1,6-glucosidase / glucan 1,4-alpha-maltotriohydrolase activity / oligo-1,6-glucosidase activity / maltose catabolic process / : / sucrose alpha-glucosidase activity / sucrose catabolic process / alpha-amylase activity / mitochondrion Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Yamamoto, K. / Miyake, H. / Kusunoki, M. / Osaki, S. | |||||||||
Citation | Journal: J.Biosci.Bioeng. / Year: 2011 Title: Steric hindrance by 2 amino acid residues determines the substrate specificity of isomaltase from Saccharomyces cerevisiae Authors: Yamamoto, K. / Miyake, H. / Kusunoki, M. / Osaki, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3axh.cif.gz | 141.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3axh.ent.gz | 107.9 KB | Display | PDB format |
PDBx/mmJSON format | 3axh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3axh_validation.pdf.gz | 796.9 KB | Display | wwPDB validaton report |
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Full document | 3axh_full_validation.pdf.gz | 800.1 KB | Display | |
Data in XML | 3axh_validation.xml.gz | 25.6 KB | Display | |
Data in CIF | 3axh_validation.cif.gz | 38.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ax/3axh ftp://data.pdbj.org/pub/pdb/validation_reports/ax/3axh | HTTPS FTP |
-Related structure data
Related structure data | 3axiC 3aj7S 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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Unit cell |
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-Components
#1: Protein | Mass: 68619.305 Da / Num. of mol.: 1 / Mutation: E277A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: D-346 / Gene: IMA1, FSP2, YGR287C / Plasmid: PKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P53051, oligo-1,6-glucosidase |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: 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: 2.44 Å3/Da / Density % sol: 49.57 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 50mM HEPES pH 7.3, 0.2M lithium acetate, 21% (w/v) PEG 3350, 0.2M isomaltose , VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 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: May 15, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→24.38 Å / Num. all: 57876 / Num. obs: 56198 / % possible obs: 97.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.8→1.83 Å / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AJ7 Resolution: 1.8→24.38 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 1.932 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R Free: 0.109 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.745 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→24.38 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.796→1.843 Å / Total num. of bins used: 20
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