1vjs

STRUCTURE OF ALPHA-AMYLASE PRECURSOR

Method: X-RAY DIFFRACTION Dmax: 86.5 Å Quality: GOOD

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

ALPHA-AMYLASE

OrganismNot specified

UniProt P06278

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 30–512 Not recorded No other associated polymer X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.70 Å R-free 0.226

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMY_BACLI
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–483; UniProt 30–512

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 1vjs

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1vjs
Deposition date deposition_date1996-10-02
Structure title titleSTRUCTURE OF ALPHA-AMYLASE PRECURSOR
Keywords keywordsHYDROLASE, GLYCOSIDASE, CARBOHYDRATE METABOLISM; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier25.23
Radius of gyration Rg (electron density) rg_electron24.14
Forward intensity I(0) i048364800.00
Molecular weight molecular_weight53524.0 kDa
Excluded volume excluded_volume66496 ų
Envelope volume envelope_volume76438 ų
Hydration-shell volume shell_volume27072 ų
Envelope diameter envelope_diameter88.6
Shell Rg shell_rg31.13
Envelope Rg envelope_rg24.30
Shape Rg shape_rg24.13
Total Rg total_rg24.92
Total atoms total_atoms3800
Residues n_residues469
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 dmax86.5
Rg (real space) rg_real25.27
Rg uncertainty (real space) rg_real_error0.58
I(0) (real space) i0_real4.8360e+07
I(0) uncertainty (real space) i0_real_error6.9370e+05
Rg (reciprocal space) rg_reciprocal25.26
I(0) (reciprocal space) i0_reciprocal48360000.0000
Solution quality estimate total_estimate0.8664
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.8
Skewness Skewness skewness0.450
Kurtosis Kurtosis kurtosis-0.148
Angular range angular_range— – 0.3150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7665000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.985

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1vjsa1
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_idd1vjsa2
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 (3 domains)

Domain ID domain_id1vjsA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1vjsA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily140
Domain ID domain_id1vjsA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II

8. Citations (2)

9. Files and Curves (10)