1ven

Crystal Structure Analysis of Y164E/maltose of Bacilus cereus Beta-amylase at pH 4.6

Method: X-RAY DIFFRACTION Dmax: 82.6 Å Quality: EXCELLENT

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

Beta-amylase

Bacillus cereus

UniProt P36924

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 31–546 Mutation:Y164E GLC alpha-D-glucopyranose × 2 CA CALCIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 4.6;291 K;PEG 6000, ammonium sulfate, potassium phosphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 2.02 Å R-free 0.229

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.

12 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AMYB_BACCE
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–516; UniProt 31–546

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 1ven

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1ven
Deposition date deposition_date2004-04-03
Structure title titleCrystal Structure Analysis of Y164E/maltose of Bacilus cereus Beta-amylase at pH 4.6
Keywords keywordsbeta-alpha-barrels, optimum pH, Y164E, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.24
Radius of gyration Rg (electron density) rg_electron25.46
Forward intensity I(0) i054636300.00
Molecular weight molecular_weight58644.0 kDa
Excluded volume excluded_volume73613 ų
Envelope volume envelope_volume86133 ų
Hydration-shell volume shell_volume28877 ų
Envelope diameter envelope_diameter87.2
Shell Rg shell_rg32.13
Envelope Rg envelope_rg25.70
Shape Rg shape_rg25.45
Total Rg total_rg26.18
Total atoms total_atoms4140
Residues n_residues516
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 dmax82.6
Rg (real space) rg_real26.24
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real5.4640e+07
I(0) uncertainty (real space) i0_real_error7.9010e+05
Rg (reciprocal space) rg_reciprocal26.24
I(0) (reciprocal space) i0_reciprocal54640000.0000
Solution quality estimate total_estimate0.9010
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary81.2
Skewness Skewness skewness0.352
Kurtosis Kurtosis kurtosis-0.402
Angular range angular_range— – 0.3000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11720000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.937

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd1vena1
Class classb — All beta proteins
Fold Fold foldb.3 — Prealbumin-like
Superfamily Superfamily superfamilyb.3.1 — Starch-binding domain-like
Family Family familyb.3.1.0 — automated matches
Domain ID domain_idd1vena2
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 (2 domains)

Domain ID domain_id1venA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily80 — Glycosidases
Domain ID domain_id1venA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)