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1ayx

CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS

Method: X-RAY DIFFRACTION Dmax: 73.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

GLUCOAMYLASE

Saccharomycopsis fibuligera

UniProt P08017

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 28–519 Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.1；50 MM ACETATE BUFFER, PH 5.1, 15 % (W/V) PEG 8000 HANGING DROP Resolution 1.70 Å R-free 0.181

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 1AYX Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2F6D Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose Deposited 2005-11-29 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 28–519（492 aa）
Not recorded PO4 PHOSPHATE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50 mM acetate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.60 Å R-free 0.160
2FBA Glucoamylase from Saccharomycopsis fibuligera at atomic resolution Deposited 2005-12-09 Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–519（492 aa）
Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；295 K；50 mM acatate buffer, 15% PEG 8K, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.10 Å R-free 0.161

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

View Construct and Data Evidence
UniProt name AMYG_SACFI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–492； UniProt 28–519

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 1ayx

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ayx
Deposition date deposition_date1997-11-12
Structure title titleCRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS
Keywords keywordsGLUCOAMYLASE, HYDROLASE, GLYCOSIDASE, POLYSACCHARIDE DEGRADATION; 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_guinier23.17 Å
Radius of gyration Rg (electron density) rg_electron21.75 Å
Forward intensity I(0) i051095400.00
Molecular weight molecular_weight54710.0 kDa
Excluded volume excluded_volume67827 ų
Envelope volume envelope_volume76969 ų
Hydration-shell volume shell_volume28438 ų
Envelope diameter envelope_diameter73.7 Å
Shell Rg shell_rg29.63 Å
Envelope Rg envelope_rg21.98 Å
Shape Rg shape_rg21.73 Å
Total Rg total_rg22.66 Å
Total atoms total_atoms3878
Residues n_residues492
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 dmax73.0 Å
Rg (real space) rg_real23.01 Å
Rg uncertainty (real space) rg_real_error0.48 Å
I(0) (real space) i0_real5.1100e+07
I(0) uncertainty (real space) i0_real_error7.5430e+05
Rg (reciprocal space) rg_reciprocal23.05 Å
I(0) (reciprocal space) i0_reciprocal51100000.0000
Solution quality estimate total_estimate0.6239
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.3 Å
Skewness Skewness skewness0.126
Kurtosis Kurtosis kurtosis-0.432
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15800000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 0.999; Sysdev: 0.171; Positv: 1.000; Valcen: 0.985; 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_idd1ayxa_
Class classa — All alpha proteins
Fold Fold folda.102 — alpha/alpha toroid
Superfamily Superfamily superfamilya.102.1 — Six-hairpin glycosidases
Family Family familya.102.1.1 — Glucoamylase

CATH v4.4 (1 domains)

Domain ID domain_id1ayxA00
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily10 —
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8. Citations (1)

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9. Files and Curves (10)