SAXSdb — 5bca

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

PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 31–546	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 31–546	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 31–546	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 31–546	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

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 5BCA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CQY STARCH BINDING DOMAIN OF BACILLUS CEREUS BETA-AMYLASE Deposited 1999-08-12	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 448–546（99 aa） Fragment：STARCH-BINDING DOMAIN	Not recorded	No recorded non-water small molecule	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

1 other PDB entries and 1 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 1–516； UniProt 31–546 Author chain B； PDBConstruct 1–516； UniProt 31–546 Author chain C； PDBConstruct 1–516； UniProt 31–546 Author chain D； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5bca
Deposition date deposition_date	1999-03-12
Structure title title	BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES
Keywords keywords	HYDROLASE, BETA-AMYLASE, RAW-STARCH BINDING DOMAIN; 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	44.41 Å
Radius of gyration Rg (electron density) rg_electron	44.05 Å
Forward intensity I(0) i0	768625000.00
Molecular weight molecular_weight	233340.0 kDa
Excluded volume excluded_volume	293080 Å³
Envelope volume envelope_volume	393240 Å³
Hydration-shell volume shell_volume	72999 Å³
Envelope diameter envelope_diameter	155.2 Å
Shell Rg shell_rg	50.90 Å
Envelope Rg envelope_rg	42.72 Å
Shape Rg shape_rg	44.05 Å
Total Rg total_rg	44.37 Å
Total atoms total_atoms	16480
Residues n_residues	2064
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	146.9 Å
Rg (real space) rg_real	44.27 Å
Rg uncertainty (real space) rg_real_error	1.11 Å
I(0) (real space) i0_real	7.6860e+08
I(0) uncertainty (real space) i0_real_error	1.3040e+07
Rg (reciprocal space) rg_reciprocal	44.41 Å
I(0) (reciprocal space) i0_reciprocal	768700000.0000
Solution quality estimate total_estimate	0.8853
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.1 Å
Skewness Skewness skewness	0.199
Kurtosis Kurtosis kurtosis	-0.406
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	108400000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.887

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)
Molecular weight formula_weight	58358.5 kDa
EC 编号 ec_number	3.2.1.2
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	17232

AVNGKGMNPDYKAYLMAPLKKIPEVTNWETFENDLRWAKQNGFYAITVDFWWGDMEKNGDQQFDFSYAQRFAQSVKNAGMKMIPIISTHQCGGNVGDDCNVPIPSWVWNQKSDDSLYFKSETGTVNKETLNPLASDVIRKEYGELYTAFAAAMKPYKDVIAKIYLSGGPAGELRYPSYTTSDGTGYPSRGKFQAYTEFAKSKFRLWVLNKYGSLNEVNKAWGTKLISELAILPPSDGEQFLMNGYLSMYGKDYLEWYQGILENHTKLIGELAHNAFDTTFQVPIGAKIAGVHWQYNNPTIPHGAEKPAGYNDYSHLLDAFKSAKLDVTFTCLEMTDKGSYPEYSMPKTLVQNIATLANEKGIVLNGENALSIGNEEEYKRVAEMAFNYNFAGFTLLRYQDVMYNNSLMGKFKDLLGVTPVMQTIVVKNVPTTIGDTVYITGNRAELGSWDTKQYPIQLYYDSHSNDWRGNVVLPAERNIEFKAFIKSKDGTVKSWQTIQQSWNPVPLKTTSHTSSW

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	752

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5bcaa1
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

Domain ID domain_id	d5bcaa2
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

Domain ID domain_id	d5bcab1
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

Domain ID domain_id	d5bcab2
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

Domain ID domain_id	d5bcac1
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

Domain ID domain_id	d5bcac2
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

Domain ID domain_id	d5bcad1
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

Domain ID domain_id	d5bcad2
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 (8 domains)

Domain ID domain_id	5bcaA01
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	5bcaA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5bcaB01
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	5bcaB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5bcaC01
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	5bcaC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5bcaD01
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	5bcaD02
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 (4)

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Unit-cell length a length_a	177.900 Å
Unit-cell length b length_b	112.900 Å
Unit-cell length c length_c	146.200 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1860
R_free r_free	0.2400

fit	/app/data/saxs_computation/bc/5bca/5bca.fit
pddf	/app/data/pr_computation/bc/5bca/5bca.pr.out
profile	/app/data/saxs_computation/bc/5bca/5bca.dat

BETA-AMYLASE FROM BACILLUS CEREUS VAR. MYCOIDES

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

PROTEIN (1,4-ALPHA-D-GLUCAN MALTOHYDROLASE.)

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