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1wdq

The role of an inner loop in the catalytic mechanism of soybean beta-amylase

Method: X-RAY DIFFRACTION Dmax: 71.3 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-amylase

Glycine max

UniProt P10538

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–495 Mutation：T342V alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 2 SO4 SULFATE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 1.28 Å R-free 0.174

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 1WDQ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BFN BETA-AMYLASE/BETA-CYCLODEXTRIN COMPLEX Deposited 1998-05-22 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 1–495（495 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.4；277 K；49% (NH4)2SO4, 0.1M NAOAC PH 5.4, 18MM 2-MERCAPTOETHANOL, AT 277K
Resolution 2.07 Å R-free 0.211
1BTC THREE-DIMENSIONAL STRUCTURE OF SOYBEAN BETA-AMYLASE DETERMINED AT 3.0 ANGSTROMS RESOLUTION: PRELIMINARY CHAIN TRACING OF THE COMPLEX WITH ALPHA-CYCLODEXTRIN Deposited 1993-02-18 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 5–495（491 aa）
Not recorded SO4 SULFATE ION × 1 BME BETA-MERCAPTOETHANOL × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å
1BYA CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1BYB CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25 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 1–495（495 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1BYC CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25 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 1–495（495 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1BYD CRYSTAL STRUCTURES OF SOYBEAN BETA-AMYLASE REACTED WITH BETA-MALTOSE AND MALTAL: ACTIVE SITE COMPONENTS AND THEIR APPARENT ROLE IN CATALYSIS Deposited 1994-01-25 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Mutation：D374Y / L481R / P487D SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.241
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–495（495 aa）
Mutation：D374Y / L481R / P487D SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.241
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–495（495 aa）
Mutation：D374Y / L481R / P487D SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.241
1UKO Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-30 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–495（495 aa）
Mutation：D374Y / L481R / P487D SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.10 Å R-free 0.241
1UKP Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-31 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Mutation：D374Y / L481R / P487D / K462S SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.10 Å R-free 0.234
1UKP Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-31 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–495（495 aa）
Mutation：D374Y / L481R / P487D / K462S SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.10 Å R-free 0.234
1UKP Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–495（495 aa）
Mutation：D374Y / L481R / P487D / K462S SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.10 Å R-free 0.234
1UKP Crystal structure of soybean beta-amylase mutant substituted at surface region Deposited 2003-08-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–495（495 aa）
Mutation：D374Y / L481R / P487D / K462S SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.10 Å R-free 0.234
1V3H The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase Deposited 2003-11-02 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Mutation：F76L, E186Q SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.60 Å R-free 0.181
1V3I The roles of Glu186 and Glu380 in the catalytic reaction of soybean beta-amylase Deposited 2003-11-02 Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Mutation：F76L, E380Q SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.90 Å R-free 0.193
1WDP The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Not recorded SO4 SULFATE ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.27 Å R-free 0.174
1WDR The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Mutation：T342S Non-standard monomer：Yes (specific site not provided by mmCIF) GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.35 Å R-free 0.172
1WDS The role of an inner loop in the catalytic mechanism of soybean beta-amylase Deposited 2004-05-17 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–495（495 aa）
Mutation：T342A GLC alpha-D-glucopyranose × 1 SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；277 K；ammonium sulfate, sodium acetate, 2-mercaptoethanol, EDTA, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.64 Å R-free 0.200

13 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMYB_SOYBN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–495； UniProt 1–495

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 1wdq

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1wdq
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1wdq
Deposition date deposition_date2004-05-17
Structure title titleThe role of an inner loop in the catalytic mechanism of soybean beta-amylase
Keywords keywords(beta/alpha)8 barrel, Hydrolase; 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_guinier23.21 Å
Radius of gyration Rg (electron density) rg_electron21.88 Å
Forward intensity I(0) i053281200.00
Molecular weight molecular_weight56885.0 kDa
Excluded volume excluded_volume71042 ų
Envelope volume envelope_volume79523 ų
Hydration-shell volume shell_volume29021 ų
Envelope diameter envelope_diameter74.5 Å
Shell Rg shell_rg29.97 Å
Envelope Rg envelope_rg22.18 Å
Shape Rg shape_rg21.86 Å
Total Rg total_rg22.83 Å
Total atoms total_atoms4006
Residues n_residues493
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 dmax71.3 Å
Rg (real space) rg_real23.06 Å
Rg uncertainty (real space) rg_real_error0.33 Å
I(0) (real space) i0_real5.3280e+07
I(0) uncertainty (real space) i0_real_error6.3740e+05
Rg (reciprocal space) rg_reciprocal23.10 Å
I(0) (reciprocal space) i0_reciprocal53280000.0000
Solution quality estimate total_estimate0.9008
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary70.2 Å
Skewness Skewness skewness0.167
Kurtosis Kurtosis kurtosis-0.415
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11730000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.982; Smooth: 0.983
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1wdqa1
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_id1wdqA00
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)