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- PDB-4j3w: Crystal structure of barley limit dextrinase (E510A mutant) in co... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4j3w | |||||||||
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Title | Crystal structure of barley limit dextrinase (E510A mutant) in complex with a branched maltohexasaccharide | |||||||||
![]() | Limit dextrinase | |||||||||
![]() | HYDROLASE / GH13 hydrolase | |||||||||
Function / homology | ![]() pullulanase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sim, L. / Windahl, M.S. / Moeller, M.S. / Henriksen, A. | |||||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 353.8 KB | Display | ![]() |
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PDB format | ![]() | 281.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4j3sC ![]() 4j3tC ![]() 4j3uC ![]() 4j3vC ![]() 4j3xC ![]() 2y4sS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 99688.688 Da / Num. of mol.: 1 / Fragment: UNP Residues 22-905 / Mutation: E510A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||||
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#2: Polysaccharide | alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-6)-[alpha-D- ...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 | ||||
#3: Chemical | ChemComp-CA / | ||||
#4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | Sequence details | THESE RESIDUES REPRESENT NATURAL VARIANTS. | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.32 % / Mosaicity: 0.59 ° |
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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: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 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: 1.666→82.924 Å / Num. all: 89214 / Num. obs: 89214 / % possible obs: 97 % / Redundancy: 4.7 % / Rsym value: 0.079 / Net I/σ(I): 12 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2Y4S Resolution: 1.67→22.83 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.1878 / WRfactor Rwork: 0.1573 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.9124 / SU B: 3.484 / SU ML: 0.054 / SU R Cruickshank DPI: 0.1545 / SU Rfree: 0.0896 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.155 / ESU R Free: 0.09 / 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: 80.44 Å2 / Biso mean: 16.0249 Å2 / Biso min: 3.24 Å2
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Refinement step | Cycle: LAST / Resolution: 1.67→22.83 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.666→1.709 Å / Total num. of bins used: 20
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