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- PDB-2xgi: Crystal structure of Barley Beta-Amylase complexed with 3,4- epox... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2xgi | |||||||||
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Title | Crystal structure of Barley Beta-Amylase complexed with 3,4- epoxybutyl alpha-D-glucopyranoside | |||||||||
![]() | BETA-AMYLASE | |||||||||
![]() | HYDROLASE / GLYCOSIDASE / CARBOHYDRATE METABOLISM / GLYCOSYL HYDROLASE FAMILY 14 / STARCH DEGRADATION / 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. / 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 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9- ... SHEET DETERMINATION METHOD: DSSP 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 | ![]() | 247.1 KB | Display | ![]() |
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PDB format | ![]() | 197 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2xffC ![]() 2xfrC ![]() 2xfyC ![]() 2xg9C ![]() 2xgbC ![]() 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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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: Chemical | #3: Sugar | ChemComp-J5B / ( | #4: Sugar | ChemComp-EBQ / ( | #5: Water | ChemComp-HOH / | Nonpolymer details | 3,4-EPOXYBUTYL ALPHA-D-GLUCOPYRANOSIDE: THE LIGAND WAS A MIXTURE OF TWO DIASTEREOISOMERS EPIMERIC ...3,4-EPOXYBUTYL | Sequence details | PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS FROM UNIPROTKB DATABASE ENTRY P16098 AT ...PROTEIN ISOLATED FROM NATURAL SOURCE BUT SEQUENCE DIFFERS FROM UNIPROTKB DATABASE ENTRY P16098 AT THREE POSITIONS. 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: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.117 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→26.13 Å / Num. obs: 109532 / % possible obs: 98 % / Observed criterion σ(I): -9 / Redundancy: 6.48 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.21 |
Reflection shell | Resolution: 1.3→1.37 Å / Redundancy: 3.88 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.48 / % possible all: 86.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1B1Y Resolution: 1.3→24.701 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.316 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.049 / ESU R Free: 0.046 / 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: 11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→24.701 Å
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Refine LS restraints |
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