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2xfr

Crystal structure of barley beta-amylase at atomic resolution

Method: X-RAY DIFFRACTION Dmax: 72.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

BETA-AMYLASE

OrganismNot specified

UniProt P16098

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–535 Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；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 Resolution 0.97 Å R-free 0.130

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2XFR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1B1Y SEVENFOLD MUTANT OF BARLEY BETA-AMYLASE Deposited 1998-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 5–504（500 aa）
Mutation：M185L,S295A,I297V,S350P,S351P,Q352D,A376S BGC beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.1；HUNGING DROP VAPOR DIFFUSION AGAINST 0.1 M PIPES PH 7.1, 0.1 M MGAC2 AND 14% PEG 6000 WITH A PROTEIN CONCENTRATION OF 3 MG/ML., vapor diffusion - hanging drop
Resolution 2.50 Å R-free 0.256
2XFF Crystal structure of Barley Beta-Amylase complexed with acarbose Deposited 2010-05-28 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–535（535 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；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
Resolution 1.31 Å R-free 0.155
2XFY Crystal structure of Barley Beta-Amylase complexed with alpha- cyclodextrin Deposited 2010-05-28 Different oligomeric state Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–535（535 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；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
Resolution 1.21 Å R-free 0.153
2XG9 Crystal structure of Barley Beta-Amylase complexed with 4-O-alpha-D- glucopyranosylmoranoline Deposited 2010-06-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–535（535 aa）
Not recorded EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；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
Resolution 1.80 Å R-free 0.171
2XGB Crystal structure of Barley Beta-Amylase complexed with 2,3- epoxypropyl-alpha-D-glucopyranoside Deposited 2010-06-02 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–535（535 aa）
Not recorded EPG (2R)-oxiran-2-ylmethyl alpha-D-glucopyranoside × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；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
Resolution 1.20 Å R-free 0.141
2XGI Crystal structure of Barley Beta-Amylase complexed with 3,4- epoxybutyl alpha-D-glucopyranoside Deposited 2010-06-04 Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–535（535 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 J5B (3R)-3-hydroxybutyl alpha-D-glucopyranoside × 1 EBQ (3S)-3-hydroxybutyl alpha-D-glucopyranoside × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；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
Resolution 1.30 Å R-free 0.158

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMYB_HORVU
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–535； UniProt 1–535

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2xfr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2xfr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2xfr
Deposition date deposition_date2010-05-28
Structure title titleCrystal structure of barley beta-amylase at atomic resolution
Keywords keywordsHYDROLASE, CARBOHYDRATE METABOLISM, GLYCOSYL HYDROLASE FAMILY 14, STARCH DEGRADATION, GERMINATION; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.16 Å
Radius of gyration Rg (electron density) rg_electron21.95 Å
Forward intensity I(0) i050450500.00
Molecular weight molecular_weight55214.0 kDa
Excluded volume excluded_volume68957 ų
Envelope volume envelope_volume78665 ų
Hydration-shell volume shell_volume28756 ų
Envelope diameter envelope_diameter74.7 Å
Shell Rg shell_rg29.75 Å
Envelope Rg envelope_rg22.09 Å
Shape Rg shape_rg21.96 Å
Total Rg total_rg22.82 Å
Total atoms total_atoms3902
Residues n_residues487
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax72.2 Å
Rg (real space) rg_real23.01 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real5.0450e+07
I(0) uncertainty (real space) i0_real_error7.2370e+05
Rg (reciprocal space) rg_reciprocal23.05 Å
I(0) (reciprocal space) i0_reciprocal50450000.0000
Solution quality estimate total_estimate0.8200
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0 Å
Skewness Skewness skewness0.133
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15310000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.891; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2xfra_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.1 — Amylase, catalytic domain

CATH v4.4 (1 domains)

Domain ID domain_id2xfrA00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
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8. Citations (1)

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9. Files and Curves (10)