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Yorodumi- PDB-2xg9: Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xg9 | ||||||
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Title | Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha-D- glucopyranosylmoranoline | ||||||
Components | BETA-AMYLASE | ||||||
Keywords | HYDROLASE / GLYCOSIDASE / CARBOHYDRATE METABOLISM / GLYCOSYL HYDROLASE FAMILY 14 / STARCH DEGRADATION / GERMINATION | ||||||
Function / homology | Function and homology information beta-amylase / beta-amylase activity / amylopectin maltohydrolase activity / polysaccharide catabolic process / identical protein binding Similarity search - Function | ||||||
Biological species | HORDEUM VULGARE (barley) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
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. | ||||||
Citation | Journal: Mol.Biosyst. / Year: 2011 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xg9.cif.gz | 133.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xg9.ent.gz | 100.9 KB | Display | PDB format |
PDBx/mmJSON format | 2xg9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/2xg9 ftp://data.pdbj.org/pub/pdb/validation_reports/xg/2xg9 | HTTPS FTP |
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-Related structure data
Related structure data | 2xffC 2xfrC 2xfyC 2xgbC 2xgiC 1b1yS 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
#1: Protein | Mass: 59670.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PROTEIN PURCHASED FROM MEGAZYME / Source: (natural) HORDEUM VULGARE (barley) / Tissue: GRAIN ENDOSPERM / References: UniProt: P16098, beta-amylase | ||||||
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#2: Chemical | ChemComp-NOJ / | ||||||
#3: Sugar | ChemComp-GLC / | ||||||
#4: Chemical | #5: Water | ChemComp-HOH / | Nonpolymer details | 4-O-ALPHA-D-GLUCOPYRANOSYLMORANOLINE: THIS IS A DISACCHARIDE INHIBITOR COMPRISED OF ALPHA-1,4- ...4-O-ALPHA-D-GLUCOPYRAN | 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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 4, 2007 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.542 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→21.81 Å / Num. obs: 41215 / % possible obs: 97.2 % / Observed criterion σ(I): -9 / Redundancy: 3.56 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 10.48 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.35 % / Rmerge(I) obs: 0.11 / Mean I/σ(I) obs: 6.31 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1B1Y Resolution: 1.8→21.115 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.46 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.111 / 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: 13.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→21.115 Å
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Refine LS restraints |
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