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- PDB-4aio: Crystal structure of the starch debranching enzyme barley limit d... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aio | ||||||
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Title | Crystal structure of the starch debranching enzyme barley limit dextrinase | ||||||
![]() | LIMIT DEXTRINASE | ||||||
![]() | HYDROLASE / PULLULANASE / GLYCOSIDE HYDROLASE FAMILY 13 | ||||||
Function / homology | ![]() pullulanase activity / polysaccharide catabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Moeller, M.S. / Abou Hachem, M. / Svensson, B. / Henriksen, A. | ||||||
![]() | ![]() Title: Structure of the Starch-Debranching Enzyme Barley Limit Dextrinase Reveals Homology of the N-Terminal Domain to Cbm21. Authors: Moeller, M.S. / Abou Hachem, M. / Svensson, B. / Henriksen, A. #1: ![]() Title: Crystal Structure of an Essential Enzyme in Seed Starch Degradation: Barley Limit Dextrinase in Complex with Cyclodextrins. Authors: Vester-Christensen, M.B. / Abou Hachem, M. / Svensson, B. / Henriksen, A. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.1 KB | Display | ![]() |
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PDB format | ![]() | 146 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 441.9 KB | Display | ![]() |
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Full document | ![]() | 446.7 KB | Display | |
Data in XML | ![]() | 33.4 KB | Display | |
Data in CIF | ![]() | 48.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2y4sS 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
#1: Protein | Mass: 97444.156 Da / Num. of mol.: 1 / Fragment: RESIDUES 22-904 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | #4: Chemical | ChemComp-IOD / #5: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | 4 AMINO ACID DISCREPANCIES. THE SEQUENCE STRETCH BETWEEN RESIDUES 484-486 REFLECTS THAT THE CLONED ...4 AMINO ACID DISCREPANC | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.45 % / Description: NONE |
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Crystal grow | Details: PROTEIN STOCK: 10 MG/ML PROTEIN 50 MM MES PH 6.6, 250 MM NACL, 0.5 MM CACL2 AND 0.67 MM MALTOTRIOSE. RESERVOIR: 30% POLYETHYLENE GLYCOL (PEG) 3350, 5% GLYCEROL, AND 0.3 M NAI. CYSTEIN WAS ...Details: PROTEIN STOCK: 10 MG/ML PROTEIN 50 MM MES PH 6.6, 250 MM NACL, 0.5 MM CACL2 AND 0.67 MM MALTOTRIOSE. RESERVOIR: 30% POLYETHYLENE GLYCOL (PEG) 3350, 5% GLYCEROL, AND 0.3 M NAI. CYSTEIN WAS ADDED TO THE DROPS TO A FINAL CONCENTRATION OF 5-7 MM |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97626 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→35.54 Å / Num. obs: 60352 / % possible obs: 91.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 2.1 / % possible all: 94.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2Y4S Resolution: 1.9→33.694 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 3.322 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.158 / 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: 20.828 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→33.694 Å
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Refine LS restraints |
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