SAXSdb — 3bga

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

Beta-galactosidase

Bacteroides thetaiotaomicron VPI-5482

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	MAGNESIUM ION × 2 SODIUM ION × 4 CHLORIDE ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8A799_BACTN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–1002； UniProt 24–1022 Author chain B； PDBConstruct 4–1002； UniProt 24–1022

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	3bga
Deposition date deposition_date	2007-11-26
Structure title title	Crystal structure of beta-galactosidase from Bacteroides thetaiotaomicron VPI-5482
Keywords keywords	;Beta-Galactosidase, NYSGXRC, Protein Structure Initiative II (PSI-II), Glycosyl hydrolase family 2, Jelly-roll fold, Immunoglobulin-like fold, Tim-barrel domain, Structural Genomics, New York SGX Research Center for Structural Genomics, HYDROLASE ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3bga__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3bga__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bga__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	40.77 Å
Rg (electron density)	40.62 Å
Total Rg	41.15 Å
Atom count	16106
Residues	1963
Excluded volume	285410 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bga__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Beta-galactosidase
Molecular weight formula_weight	116190.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	17243

MSLKQPLPEWQSQYAVGLNKLAPHTYVWPYADASDIGKPGGYEQSPYYMSLNGKWKFNWVKNPDNRPKDFYQPSYYTGGWADINVPGNWERQGYGTAIYVNETYEFDDKMFNFKKNPPLVPFAENEVGSYRRTFKVPADWKGRRVVLCCEGVISFYYVWVNGKLLGYNQGSKTAAEWDITDVLSEGENVVALEVYRWSSGAYLECQDMWRLSGIERDVYLYSTPKQYIADYKVSASLDKEKYKEGIFNLEVTVEGPSATASSIAYTLKDASGKAVLQDAINIKSRGLSNFIAFDEKKIAEVKAWNAEHPNLYTLVLELKDAQGKVTELTGCEVGFRTSEIKDGRFCINGVPVLVKGTNRHEHSQLGRTVSKELMEQDIRLMKQHNINMVRNSHYPTHPYWYQLCDRYGLYMIDEANIESHGMGYGPASLAKDSTWLTAHMDRTHRMYERSKNHPAIVIWSQGNEAGNGINFERTYDWLKSVEKGRPVQYERAELNYNTDIYCRMYRSVDEIKAYVGKKDIYRPFILCEYLHAMGNSCGGMKEYWEVFENEPMAQGGCIWDWVDQNFREIDKDGKWYWTYGGDYGPEGIPSFGNFCGNGLVNAVREPHPHLLEVKKIYQNIKATLSDRKNLKVCIKNWYDFSNLNEYILRWNVKGEDGTVLAEGTKEVDCEPHATVDVTLGAVKLPNTVREAYLNLSWSRKEATPLVDTDWEVAYDQFVLAGNKNTTAYRPQKAGETAFVVDKNTGALSSLTLDGKELLAAPITLSLFRPATDNDNRDRNGARLWRKAGLNNLTQKVVSLKEEKTSATVRAEILNGKGQKVGMADFVYALDKNGALKVRTTFQPDTAIVKSMARLGLTFRMADAYNQVSYLGRGDHETYIDRNQSGRIGLYDTTVERMFHYYATPQSTANRTDVRWAKLTDQAGEGVFMESNRPFQFSIIPFSDVLLEKAHHINELERDGMITIHLDAEQAGVGTATCGPGVLPQYLVPVKKQSFEFTLYPVKEGHHHHHH

Source Source

Source organism organism	Bacteroides thetaiotaomicron VPI-5482
NCBI taxonomy ID ncbi_taxonomy_id	226186
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1137

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id	3bgaA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3bgaA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3bgaA03
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	3bgaA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3bgaA05
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3bgaB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	260 — Galactose-binding domain-like

Domain ID domain_id	3bgaB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3bgaB03
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	3bgaB04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3bgaB05
Class class	2 — Mainly Beta
Architecture architecture	70 — Distorted Sandwich
Topology topology	98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	88.335 Å
Unit-cell length b length_b	138.864 Å
Unit-cell length c length_c	102.818 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	109.73 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	49.760 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2340

Crystal structure of beta-galactosidase from Bacteroides thetaiotaomicron VPI-5482

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

Beta-galactosidase

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bga__assembly_1__model_1

3bga__assembly_1__model_1 | I(q)

3bga__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)

Crystal structure of beta-galactosidase from Bacteroides thetaiotaomicron VPI-5482

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

Beta-galactosidase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3bga__assembly_1__model_1

3bga__assembly_1__model_1 | I(q)

3bga__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

7. Citations (1)