+Open data
-Basic information
Entry | Database: PDB / ID: 3a4a | ||||||
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Title | Crystal structure of isomaltase from Saccharomyces cerevisiae | ||||||
Components | Oligo-1,6-glucosidase | ||||||
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: 1.6 Å | ||||||
Authors | Yamamoto, K. / Miyake, H. / Kusunoki, M. / Osaki, S. | ||||||
Citation | Journal: Febs J. / Year: 2010 Title: Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose 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 | 3a4a.cif.gz | 144.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a4a.ent.gz | 110.7 KB | Display | PDB format |
PDBx/mmJSON format | 3a4a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3a4a_validation.pdf.gz | 437.3 KB | Display | wwPDB validaton report |
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Full document | 3a4a_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | 3a4a_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 3a4a_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/3a4a ftp://data.pdbj.org/pub/pdb/validation_reports/a4/3a4a | HTTPS FTP |
-Related structure data
Related structure data | 3aj7C 3a47S 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: 68677.336 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: D-346 / Plasmid: pKP1500 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P53051, oligo-1,6-glucosidase |
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#2: Sugar | ChemComp-GLC / |
#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: 2.47 Å3/Da / Density % sol: 50.19 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 19% PEG 3350, 0.05M HEPES, 0.2M lithium acetate, 0.2M maltose, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 288K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å |
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Apr 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→25 Å / Num. all: 87616 / Num. obs: 87353 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 0.042 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.05 / Mean I/σ(I) obs: 13.8 / Num. unique all: 8761 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3A47 Resolution: 1.6→23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.077 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.073 / 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: 11.85 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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