← Back to search
1fa2

CRYSTAL STRUCTURE OF BETA-AMYLASE FROM SWEET POTATO

Method: X-RAY DIFFRACTION Dmax: 74.8 Å Quality: GOOD
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

BETA-AMYLASE

OrganismNot specified

UniProt P10537

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 Homooligomer Protein × 4 其他Polymer 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–498 Not recorded alpha-D-glucopyranose-(1-4)-2-deoxy-beta-D-arabino-hexopyranose × 4 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；298 K；20% Polyethyleneglycol 1500, 50 mM CaCl2, 150 mM sodium 4-touene sulfonate, pH 6.5, vapor diffusion, temperature 298.0K Resolution 2.30 Å R-free 0.281

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 1FA2 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5WQS Crystal structure of Apo Beta-Amylase from Sweet potato Deposited 2016-11-28 Different construct 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 2–499（498 aa） Fragment：UNP residues 2-499
Not recorded IPA ISOPROPYL ALCOHOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；0.1M Sodium acetate (pH 5.5), 0.05M Tris (pH 7.5), 0.01M NaCl, 2% Isoproponal, 18% PEG 4000
Resolution 1.90 Å R-free 0.202
5WQU Crystal structure of Sweet Potato Beta-Amylase complexed with Maltotetraose Deposited 2016-11-28 Different construct 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 2–499（498 aa） Fragment：UNP residues 2-499
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；0.1M Na Acetate (pH 5.5), 0.05M Tris (pH 7.5), 0.01M NaCl, 2% Isopropanol and 18% PEG 4000
Resolution 2.49 Å R-free 0.245

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMYB_IPOBA
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–498； UniProt 1–498

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 1fa2

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1fa2
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id1fa2
Deposition date deposition_date2000-07-12
Structure title titleCRYSTAL STRUCTURE OF BETA-AMYLASE FROM SWEET POTATO
Keywords keywordsTIM barrel, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier23.41 Å
Radius of gyration Rg (electron density) rg_electron22.32 Å
Forward intensity I(0) i051922400.00
Molecular weight molecular_weight55859.0 kDa
Excluded volume excluded_volume69681 ų
Envelope volume envelope_volume81271 ų
Hydration-shell volume shell_volume29285 ų
Envelope diameter envelope_diameter79.4 Å
Shell Rg shell_rg30.27 Å
Envelope Rg envelope_rg22.57 Å
Shape Rg shape_rg22.31 Å
Total Rg total_rg23.21 Å
Total atoms total_atoms3934
Residues n_residues498
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
▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax74.8 Å
Rg (real space) rg_real23.26 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real5.1920e+07
I(0) uncertainty (real space) i0_real_error6.6620e+05
Rg (reciprocal space) rg_reciprocal23.30 Å
I(0) (reciprocal space) i0_reciprocal51920000.0000
Solution quality estimate total_estimate0.8908
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8 Å
Skewness Skewness skewness0.180
Kurtosis Kurtosis kurtosis-0.390
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14620000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.998
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1fa2a_
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_id1fa2A00
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
▶

8. Citations (1)

▶

9. Files and Curves (10)