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- PDB-2xfy: Crystal structure of Barley Beta-Amylase complexed with alpha- cy... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xfy | |||||||||
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Title | Crystal structure of Barley Beta-Amylase complexed with alpha- cyclodextrin | |||||||||
![]() | BETA-AMYLASE | |||||||||
![]() | HYDROLASE / CARBOHYDRATE METABOLISM / GERMINATION | |||||||||
Function / homology | ![]() beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / identical protein binding Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rejzek, M. / Stevenson, C.E.M. / Southard, A.M. / Stanley, D. / Denyer, K. / Smith, A.M. / Naldrett, M.J. / Lawson, D.M. / Field, R.A. | |||||||||
![]() | ![]() Title: Chemical Genetics and Cereal Starch Metabolism: Structural Basis of the Non-Covalent and Covalent Inhibition of Barley Beta-Amylase. Authors: Rejzek, M. / Stevenson, C.E.M. / Southard, A.M. / Stanley, D. / Denyer, K. / Smith, A.M. / Naldrett, M.J. / Lawson, D.M. / Field, R.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 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 | ![]() | 254.2 KB | Display | ![]() |
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PDB format | ![]() | 203.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 992.6 KB | Display | ![]() |
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Full document | ![]() | 1002.8 KB | Display | |
Data in XML | ![]() | 29.9 KB | Display | |
Data in CIF | ![]() | 48.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2xffC ![]() 2xfrC ![]() 2xg9C ![]() 2xgbC ![]() 2xgiC ![]() 1b1yS 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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1 |
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Unit cell |
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Components
#1: Protein | Mass: 59670.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PROTEIN PURCHASED FROM MEGAZYME / Source: (natural) ![]() ![]() | ||||||
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#2: Polysaccharide | Cyclohexakis-(1-4)-(alpha-D-glucopyranose) / alpha-cyclodextrin | ||||||
#3: Chemical | #4: Water | ChemComp-HOH / | Nonpolymer details | 1,2-ETHANEDIOL (EDO): PRESENT AT 20 PERCENT IN THE CRYOPROTECTANT ALPHA-CYCLODEXTRIN (CYCLOHEXA- ...1,2-ETHANEDIOL | Sequence details | PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS AT 3 POSITIONS TO UNIPROTKB DATABASE ...PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS AT 3 POSITIONS TO UNIPROTKB DATABASE ENTRY P16098. THESE CHANGES WERE IDENTIFIED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.91 Å3/Da / Density % sol: 35.6 % / Description: NONE |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: CRYSTALS WERE GROWN AT 291 K USING THE HANGING DROP VAPOUR DIFFUSION METHOD WITH PROTEIN AT 10 MG PER ML AND A PRECIPITANT COMPRISED OF 14 PERCENT PEG 3350 IN 100 MM BIS-TRIS PROPANE BUFFER AT PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9507 Å / Relative weight: 1 |
Reflection | Resolution: 1.19→28.09 Å / Num. obs: 139370 / % possible obs: 98.4 % / Observed criterion σ(I): -9 / Redundancy: 5.19 % / Biso Wilson estimate: 9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.31 |
Reflection shell | Resolution: 1.19→1.26 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.46 / % possible all: 90.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B1Y Resolution: 1.207→25.76 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.05 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.037 / ESU R Free: 0.037 / 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: 1.4 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.207→25.76 Å
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