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2fba

Glucoamylase from Saccharomycopsis fibuligera at atomic resolution

Method: X-RAY DIFFRACTION Dmax: 71.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glucoamylase GLU1

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：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

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 2FBA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AYX CRYSTAL STRUCTURE OF GLUCOAMYLASE FROM SACCHAROMYCOPSIS FIBULIGERA AT 1.7 ANGSTROMS Deposited 1997-11-12 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 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
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

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 2fba

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id2fba
Deposition date deposition_date2005-12-09
Structure title titleGlucoamylase from Saccharomycopsis fibuligera at atomic resolution
Keywords keywords(alpha-alpha)6 barrel, TRIS, 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_guinier22.94 Å
Radius of gyration Rg (electron density) rg_electron21.53 Å
Forward intensity I(0) i051046200.00
Molecular weight molecular_weight54710.0 kDa
Excluded volume excluded_volume67827 ų
Envelope volume envelope_volume75866 ų
Hydration-shell volume shell_volume28202 ų
Envelope diameter envelope_diameter73.3 Å
Shell Rg shell_rg29.47 Å
Envelope Rg envelope_rg21.82 Å
Shape Rg shape_rg21.51 Å
Total Rg total_rg22.45 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 dmax71.1 Å
Rg (real space) rg_real22.78 Å
Rg uncertainty (real space) rg_real_error0.34 Å
I(0) (real space) i0_real5.1050e+07
I(0) uncertainty (real space) i0_real_error5.8730e+05
Rg (reciprocal space) rg_reciprocal22.82 Å
I(0) (reciprocal space) i0_reciprocal51050000.0000
Solution quality estimate total_estimate0.8971
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary30.6 Å
Skewness Skewness skewness0.124
Kurtosis Kurtosis kurtosis-0.435
Angular range angular_range— – 0.3450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15120000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.995
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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_idd2fbaa_
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_id2fbaA00
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)