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Yorodumi- PDB-4j3x: Crystal structure of barley limit dextrinase (E510A mutant) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j3x | |||||||||
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Title | Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltoheptasaccharide | |||||||||
Components | Limit dextrinase | |||||||||
Keywords | HYDROLASE / GH13 hydrolase | |||||||||
Function / homology | Function and homology information pullulanase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | Hordeum vulgare (barley) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | |||||||||
Authors | Sim, L. / Windahl, M.S. / Moeller, M.S. / Henriksen, A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Oligosaccharide and substrate binding in the starch debranching enzyme barley limit dextrinase Authors: Moeller, M.S. / Windahl, M.S. / Sim, L. / Bjstrup, M. / Abou Hachem, M. / Hindsgaul, O. / Palcic, M. / Svensson, B. / Henriksen, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j3x.cif.gz | 391.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j3x.ent.gz | 315.3 KB | Display | PDB format |
PDBx/mmJSON format | 4j3x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j3x_validation.pdf.gz | 706.9 KB | Display | wwPDB validaton report |
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Full document | 4j3x_full_validation.pdf.gz | 710.2 KB | Display | |
Data in XML | 4j3x_validation.xml.gz | 40.2 KB | Display | |
Data in CIF | 4j3x_validation.cif.gz | 63.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j3/4j3x ftp://data.pdbj.org/pub/pdb/validation_reports/j3/4j3x | HTTPS FTP |
-Related structure data
Related structure data | 4j3sC 4j3tC 4j3uC 4j3vC 4j3wC 2y4sS C: citing same article (ref.) S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 99688.688 Da / Num. of mol.: 1 / Fragment: Residues 22-905 / Mutation: E510A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hordeum vulgare (barley) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9FYY0, pullulanase |
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#2: Polysaccharide | alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Non-polymers , 4 types, 994 molecules
#3: Chemical | ChemComp-CA / | ||||
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#4: Chemical | ChemComp-IOD / #5: Chemical | ChemComp-CL / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | THESE RESIDUES REPRESENT NATURAL VARIANTS. |
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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: 2.29 Å3/Da / Density % sol: 46.36 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% PEG 3350, 0.3M NaI, vapor diffusion, hanging drop, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 30, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→30 Å / Num. obs: 89001 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.687 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 11.95 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2Y4S Resolution: 1.75→28.34 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.1311 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8882 / SU B: 4.885 / SU ML: 0.07 / SU R Cruickshank DPI: 0.2036 / SU Rfree: 0.1072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.204 / ESU R Free: 0.107 / 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: 74.71 Å2 / Biso mean: 18.3443 Å2 / Biso min: 5.29 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→28.34 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.746→1.791 Å / Total num. of bins used: 20
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