SAXSdb — 1bag

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

ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE

Bacillus subtilis

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 Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 42–466	Mutation：E208Q	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ; × 1 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 10% PEG 3350, 3.5 MM CALCIUM CHLORIDE, 10 MM TRIS/HCL, PH 7.5.	Resolution 2.50 Å R-free 0.252

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 1BAG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1UA7 Crystal Structure Analysis of Alpha-Amylase from Bacillus Subtilis complexed with Acarbose Deposited 2003-03-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 45–466（422 aa） Fragment：residues 4-425	Mutation：N356Q	ACI 6-AMINO-4-HYDROXYMETHYL-CYCLOHEX-4-ENE-1,2,3-TRIOL × 2 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；PEG 3350, calcium chloride, Tris-HCl, acarbose, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.21 Å R-free 0.265

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AMY_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–425； UniProt 42–466

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	1bag
Deposition date deposition_date	1998-01-30
Structure title title	ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE
Keywords keywords	ALPHA-AMYLASE, BACILLUS SUBTILIS, MALTOPENTAOSE, CATALYTIC-SITE MUTANT; ALPHA-AMYLASE
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	22.87 Å
Radius of gyration Rg (electron density) rg_electron	21.81 Å
Forward intensity I(0) i0	41907500.00
Molecular weight molecular_weight	47963.0 kDa
Excluded volume excluded_volume	58886 Å³
Envelope volume envelope_volume	65719 Å³
Hydration-shell volume shell_volume	25176 Å³
Envelope diameter envelope_diameter	79.8 Å
Shell Rg shell_rg	28.93 Å
Envelope Rg envelope_rg	22.06 Å
Shape Rg shape_rg	21.79 Å
Total Rg total_rg	22.62 Å
Total atoms total_atoms	3381
Residues n_residues	425
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	78.4 Å
Rg (real space) rg_real	22.85 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	4.1910e+07
I(0) uncertainty (real space) i0_real_error	5.6060e+05
Rg (reciprocal space) rg_reciprocal	22.86 Å
I(0) (reciprocal space) i0_reciprocal	41910000.0000
Solution quality estimate total_estimate	0.8650
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	77.2 Å
Skewness Skewness skewness	0.394
Kurtosis Kurtosis kurtosis	-0.140
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11400000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	ALPHA-1,4-GLUCAN-4-GLUCANOHYDROLASE
Molecular weight formula_weight	47067.3 kDa
EC 编号 ec_number	3.2.1.1
Mutation mutation	E208Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3527

LTAPSIKSGTILHAWNWSFNTLKHNMKDIHDAGYTAIQTSPINQVKEGNQGDKSMSNWYWLYQPTSYQIGNRYLGTEQEFKEMCAAAEEYGIKVIVDAVINHTTFDYAAISNEVKSIPNWTHGNTQIKNWSDRWDVTQNSLLGLYDWNTQNTQVQSYLKRFLERALNDGADGFRFDAAKHIELPDDGSYGSQFWPNITNTSAEFQYGQILQDSASRDAAYANYMDVTASNYGHSIRSALKNRNLGVSNISHYASDVSADKLVTWVESHDTYANDDEESTWMSDDDIRLGWAVIASRSGSTPLFFSRPEGGGNGVRFPGKSQIGDRGSALFEDQAITAVNRFHNVMAGQPEELSNPNGNNQIFMNQRGSHGVVLANAGSSSVSINTATKLPDGRYDNKAGAGSFQVNDGKLTGTINARSVAVLYPD

来源 Source

来源生物 organism	Bacillus subtilis
NCBI Class编号 ncbi_taxonomy_id	1423
宿主生物 host_organism	Bacillus subtilis

Entity 2 Entity 2 branched

Description description	;alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose ;
Molecular weight formula_weight	828.7 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 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	146

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1baga1
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	d1baga2
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	1bagA01
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	1bagA02
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 (4)

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Unit-cell length a length_a	72.590 Å
Unit-cell length b length_b	74.060 Å
Unit-cell length c length_c	117.010 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	7.000 Å
R factor r_factor	0.1980
R_work r_work	0.1980
R_free r_free	0.2520

fit	/app/data/saxs_computation/ba/1bag/1bag.fit
pddf	/app/data/pr_computation/ba/1bag/1bag.pr.out
profile	/app/data/saxs_computation/ba/1bag/1bag.dat

ALPHA-AMYLASE FROM BACILLUS SUBTILIS COMPLEXED WITH MALTOPENTAOSE

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

ALPHA-1,4-GLUCAN-4-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