1g1y

CRYSTAL STRUCTURE OF ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47 AND BETA-CYCLODEXTRIN COMPLEX

Method: X-RAY DIFFRACTION Dmax: 107.4 Å Quality: GOOD

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

ALPHA-AMYLASE II

Thermoactinomyces vulgaris

UniProt Q08751

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 × 2 其他Polymer 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–585 Chain B; UniProt 1–585 Mutation:E354A Cycloheptakis-(1-4)-(alpha-D-glucopyranose) × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.1;284 K;MES, PEG6000, Calcium chloride, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 284K Resolution 3.00 Å R-free 0.260

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.

15 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEPU2_THEVU
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–585; UniProt 1–585 Author chain B; PDBConstruct 1–585; UniProt 1–585

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 1g1y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1g1y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1g1y
Deposition date deposition_date2000-10-16
Structure title titleCRYSTAL STRUCTURE OF ALPHA-AMYLASE II (TVAII) FROM THERMOACTINOMYCES VULGARIS R-47 AND BETA-CYCLODEXTRIN COMPLEX
Keywords keywordshydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.79
Radius of gyration Rg (electron density) rg_electron32.96
Forward intensity I(0) i0285923000.00
Molecular weight molecular_weight137080.0 kDa
Excluded volume excluded_volume171470 ų
Envelope volume envelope_volume205210 ų
Hydration-shell volume shell_volume50897 ų
Envelope diameter envelope_diameter113.3
Shell Rg shell_rg40.88
Envelope Rg envelope_rg32.83
Shape Rg shape_rg32.93
Total Rg total_rg33.60
Total atoms total_atoms9698
Residues n_residues1170
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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 dmax107.4
Rg (real space) rg_real33.72
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real2.8590e+08
I(0) uncertainty (real space) i0_real_error4.4560e+06
Rg (reciprocal space) rg_reciprocal33.76
I(0) (reciprocal space) i0_reciprocal285900000.0000
Solution quality estimate total_estimate0.8981
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary38.9
Skewness Skewness skewness0.283
Kurtosis Kurtosis kurtosis-0.438
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha76930000.0000
Real-space data points n_real_points48
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: 1.000; Smooth: 0.929

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd1g1ya1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.2 — E-set domains of sugar-utilizing enzymes
Domain ID domain_idd1g1ya2
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain
Domain ID domain_idd1g1ya3
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
Domain ID domain_idd1g1yb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.2 — E-set domains of sugar-utilizing enzymes
Domain ID domain_idd1g1yb2
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain
Domain ID domain_idd1g1yb3
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 (8 domains)

Domain ID domain_id1g1yA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1g1yA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1g1yA03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology400 — Oligo-1,6-glucosidase; domain 2
Homologous superfamily homologous superfamily10 — Oligo-1,6-glucosidase; Domain 2
Domain ID domain_id1g1yA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
Domain ID domain_id1g1yB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1g1yB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1g1yB03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology400 — Oligo-1,6-glucosidase; domain 2
Homologous superfamily homologous superfamily10 — Oligo-1,6-glucosidase; Domain 2
Domain ID domain_id1g1yB04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II

8. Citations (1)

9. Files and Curves (10)