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5wqs

Crystal structure of Apo Beta-Amylase from Sweet potato

Method: X-RAY DIFFRACTION Dmax: 75.0 Å Quality: GOOD
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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 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 2–499 Fragment：UNP residues 2-499 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

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 5WQS Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FA2 CRYSTAL STRUCTURE OF BETA-AMYLASE FROM SWEET POTATO Deposited 2000-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–498（498 aa）
Not recorded 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
5WQU Crystal structure of Sweet Potato Beta-Amylase complexed with Maltotetraose Deposited 2016-11-28 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 2–499

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 5wqs

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5wqs
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5wqs
Deposition date deposition_date2016-11-28
Structure title titleCrystal structure of Apo Beta-Amylase from Sweet potato
Keywords keywordsAmylase, Apo, Sweet potato, 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_guinier23.45 Å
Radius of gyration Rg (electron density) rg_electron22.32 Å
Forward intensity I(0) i050539300.00
Molecular weight molecular_weight55791.0 kDa
Excluded volume excluded_volume69874 ų
Envelope volume envelope_volume80822 ų
Hydration-shell volume shell_volume29104 ų
Envelope diameter envelope_diameter77.8 Å
Shell Rg shell_rg30.28 Å
Envelope Rg envelope_rg22.59 Å
Shape Rg shape_rg22.31 Å
Total Rg total_rg23.23 Å
Total atoms total_atoms3933
Residues n_residues496
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 dmax75.0 Å
Rg (real space) rg_real23.30 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real5.0540e+07
I(0) uncertainty (real space) i0_real_error6.4390e+05
Rg (reciprocal space) rg_reciprocal23.34 Å
I(0) (reciprocal space) i0_reciprocal50540000.0000
Solution quality estimate total_estimate0.8909
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.0 Å
Skewness Skewness skewness0.169
Kurtosis Kurtosis kurtosis-0.399
Angular range angular_range— – 0.3400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14550000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.994
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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_idd5wqsa_
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_id5wqsA00
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)