SAXSdb — 1cqy

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

BETA-AMYLASE

Bacillus cereus

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 448–546	Fragment：STARCH-BINDING DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 18K	Resolution 1.95 Å R-free 0.225

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 1CQY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5BCA BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES Deposited 1999-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 31–546（516 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.0	Resolution 2.20 Å R-free 0.240
5BCA BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES Deposited 1999-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 31–546（516 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.0	Resolution 2.20 Å R-free 0.240
5BCA BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES Deposited 1999-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 31–546（516 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.0	Resolution 2.20 Å R-free 0.240
5BCA BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES Deposited 1999-03-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 31–546（516 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；pH 9.0	Resolution 2.20 Å R-free 0.240

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q9Z4N9_BACCE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–99； UniProt 448–546

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1cqy
Deposition date deposition_date	1999-08-12
Structure title title	STARCH BINDING DOMAIN OF BACILLUS CEREUS BETA-AMYLASE
Keywords keywords	STARCH-BINDING DOMAIN, B-AMYLASE, 3D STRUCTURE, HYDROLASE; 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	14.49 Å
Radius of gyration Rg (electron density) rg_electron	13.19 Å
Forward intensity I(0) i0	2609950.00
Molecular weight molecular_weight	11301.0 kDa
Excluded volume excluded_volume	14189 Å³
Envelope volume envelope_volume	15600 Å³
Hydration-shell volume shell_volume	10353 Å³
Envelope diameter envelope_diameter	47.2 Å
Shell Rg shell_rg	18.71 Å
Envelope Rg envelope_rg	13.60 Å
Shape Rg shape_rg	13.14 Å
Total Rg total_rg	14.60 Å
Total atoms total_atoms	800
Residues n_residues	99
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	49.3 Å
Rg (real space) rg_real	14.43 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	2.6100e+06
I(0) uncertainty (real space) i0_real_error	3.0620e+04
Rg (reciprocal space) rg_reciprocal	14.44 Å
I(0) (reciprocal space) i0_reciprocal	2610000.0000
Solution quality estimate total_estimate	0.8713
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.5 Å
Skewness Skewness skewness	0.210
Kurtosis Kurtosis kurtosis	-0.286
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	397700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.779; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.990

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1cqya_
Class class	b — All beta proteins
Fold Fold fold	b.3 — Prealbumin-like
Superfamily Superfamily superfamily	b.3.1 — Starch-binding domain-like
Family Family family	b.3.1.1 — Starch-binding domain

CATH v4.4 (1 domains)

Domain ID domain_id	1cqyA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	60.195 Å
Unit-cell length b length_b	60.195 Å
Unit-cell length c length_c	64.922 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1810
R_work r_work	0.1810
R_free r_free	0.2250

Description description	BETA-AMYLASE
Molecular weight formula_weight	11310.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	907

STARCH BINDING DOMAIN OF BACILLUS CEREUS BETA-AMYLASE

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

BETA-AMYLASE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Bacillus cereus
NCBI Class编号 ncbi_taxonomy_id	1396
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

fit	/app/data/saxs_computation/cq/1cqy/1cqy.fit
pddf	/app/data/pr_computation/cq/1cqy/1cqy.pr.out
profile	/app/data/saxs_computation/cq/1cqy/1cqy.dat