1wzk

Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) mutatnt D465N

Method: X-RAY DIFFRACTION Dmax: 109.3 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 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–585 Chain B; UniProt 1–585 Mutation:D465N CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.1;293 K;PEG6000, calcium chloride, Tris, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.30 Å R-free 0.248

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 1wzk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1wzk
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1wzk
Deposition date deposition_date2005-03-06
Structure title titleThermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) mutatnt D465N
Keywords keywordsalpha-amylase, pullulan, GH-13, alpha-amylase family, hydrolase; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier33.89
Radius of gyration Rg (electron density) rg_electron33.05
Forward intensity I(0) i0277298000.00
Molecular weight molecular_weight134950.0 kDa
Excluded volume excluded_volume168850 ų
Envelope volume envelope_volume204180 ų
Hydration-shell volume shell_volume50599 ų
Envelope diameter envelope_diameter115.0
Shell Rg shell_rg40.78
Envelope Rg envelope_rg32.93
Shape Rg shape_rg33.01
Total Rg total_rg33.71
Total atoms total_atoms9552
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 dmax109.3
Rg (real space) rg_real33.82
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real2.7730e+08
I(0) uncertainty (real space) i0_real_error4.5070e+06
Rg (reciprocal space) rg_reciprocal33.87
I(0) (reciprocal space) i0_reciprocal277300000.0000
Solution quality estimate total_estimate0.8964
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.5
Skewness Skewness skewness0.287
Kurtosis Kurtosis kurtosis-0.426
Angular range angular_range— – 0.2350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha64060000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.963

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_idd1wzka1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches
Domain ID domain_idd1wzka2
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.0 — automated matches
Domain ID domain_idd1wzka3
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_idd1wzkb1
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.18 — E set domains
Family Family familyb.1.18.0 — automated matches
Domain ID domain_idd1wzkb2
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.0 — automated matches
Domain ID domain_idd1wzkb3
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_id1wzkA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1wzkA02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1wzkA03
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_id1wzkA04
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
Domain ID domain_id1wzkB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id1wzkB02
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1wzkB03
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_id1wzkB04
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)