SAXSdb — 1bg9

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

1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE

OrganismNot specified

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 25–427	Not recorded	;4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose ; × 2 CA CALCIUM ION × 6 AF1 4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；pH 6.7	Resolution 2.80 Å R-free 0.249

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 1BG9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AMY CRYSTAL AND MOLECULAR STRUCTURE OF BARLEY ALPHA-AMYLASE Deposited 1994-03-10	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–427（403 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1AVA AMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED Deposited 1997-09-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 25–427（403 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；pH 6.7	Resolution 1.90 Å R-free 0.269
1AVA AMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED Deposited 1997-09-15	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–427（403 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；pH 6.7	Resolution 1.90 Å R-free 0.269

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMY2_HORVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–403； UniProt 25–427

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1bg9
Deposition date deposition_date	1998-06-05
Structure title title	BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE
Keywords keywords	HYDROLASE, O-GLYCOSYL; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.77 Å
Radius of gyration Rg (electron density) rg_electron	21.71 Å
Forward intensity I(0) i0	34833000.00
Molecular weight molecular_weight	45839.0 kDa
Excluded volume excluded_volume	57282 Å³
Envelope volume envelope_volume	62610 Å³
Hydration-shell volume shell_volume	24234 Å³
Envelope diameter envelope_diameter	79.7 Å
Shell Rg shell_rg	28.68 Å
Envelope Rg envelope_rg	21.97 Å
Shape Rg shape_rg	21.66 Å
Total Rg total_rg	22.64 Å
Total atoms total_atoms	3242
Residues n_residues	403
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	78.2 Å
Rg (real space) rg_real	22.76 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	3.4830e+07
I(0) uncertainty (real space) i0_real_error	5.2310e+05
Rg (reciprocal space) rg_reciprocal	22.76 Å
I(0) (reciprocal space) i0_reciprocal	34830000.0000
Solution quality estimate total_estimate	0.8668
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.1 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.153
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7370000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.766; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE
Molecular weight formula_weight	44986.4 kDa
EC 编号 ec_number	3.2.1.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3390

QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI

Entity 2 Entity 2 branched

Description description	;4,6-dideoxy-4-{[(1S,5R,6S)-3-formyl-5,6-dihydroxy-4-oxocyclohex-2-en-1-yl]amino}-alpha-D-xylo-hex-5-enopyranose-(1-4)-beta-D-glucopyranose ;
Molecular weight formula_weight	477.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 4 Entity 4 non-polymer

Description description	4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-beta-D-glucopyranose
Molecular weight formula_weight	321.3 kDa
Source method src_method	man
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	148

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1bg9a1
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

Domain ID domain_id	d1bg9a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	1bg9A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1bg9A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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8. Citations (2)

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Unit-cell length a length_a	135.200 Å
Unit-cell length b length_b	135.200 Å
Unit-cell length c length_c	79.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1510
R_work r_work	0.1510
R_free r_free	0.2490

fit	/app/data/saxs_computation/bg/1bg9/1bg9.fit
pddf	/app/data/pr_computation/bg/1bg9/1bg9.pr.out
profile	/app/data/saxs_computation/bg/1bg9/1bg9.dat

BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE

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

1,4-ALPHA-D-GLUCAN GLUCANOHYDROLASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction