SAXSdb — 3cmg

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

Putative beta-galactosidase

Bacteroides fragilis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	PHOSPHATE ION × 4 CHLORIDE ION × 4 (4S)-2-METHYL-2,4-PENTANEDIOL × 12 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LIC7_BACFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–659； UniProt 38–693

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	3cmg
Deposition date deposition_date	2008-03-21
Structure title title	Crystal structure of putative beta-galactosidase from Bacteroides fragilis
Keywords keywords	;structural genomics, Putative beta-galactosidase, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, 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.

3cmg__assembly_1__model_1

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

Download this curve (.dat)

3cmg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cmg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	42.88 Å
Rg (electron density)	42.69 Å
Total Rg	43.32 Å
Atom count	21548
Residues	2644
Excluded volume	380640 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cmg__assembly_1__model_1`	tetrameric （4）	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	Putative beta-galactosidase
Molecular weight formula_weight	76688.4 kDa
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	5977

MSLRQDILLNNNWNFRFSHQVQGDTRRVDLPHTWNAQDALAGKIDYKRGIGNYEKALYIRPEWKGKRLFLRFDGVNSIADVFINRKHIGEHRGGYGAFIFEITDLVKYGEKNSVLVRANNGEQLDIMPLVGDFNFYGGIYRDVHLLITDETCISPLDYASPGVYLVQEVVSPQEAKVCAKVNLSNRAADGTAELQVLVTDGTKVICKESRNVSLKQGADILEQLPLLIQKPRLWNGCEDPFMYQVSISLHKDGKQIDSVTQPLGLRYYHTDPDKGFFLNGKHLPLHGVCRHQDRAEVGNALRPQHHEEDVALMREMGVNAIRLAHYPQATYMYDLMDKHGIVTWAEIPFVGPGGYADKGFVDQASFRENGKQQLIELIRQHYNHPSICFWGLFNELKEVGDNPVEYVKELNALAKQEDPTRPTTSASNQDGNLNFITENIAWNRYDGWYGSTPKTLATFLDRTHKKHPELRIGISEYGAGASIYHQQDSLKQPSASGWWHPENWQTYYHMENWKIIAERPFVWGTFVWNMFDFGAAHRTEGDRPGINDKGLVTFDRKVRKDAFYFYKANWNKQEPMIYLAEKRCRLRYQPEQTFMAFTTAPEAELFVNGVSCGKQKADTYSTVVWKNVKLTSGENIIRVTTPGKKPLTDEVTVEYKEDREGHHHHHH

Source Source

Source organism organism	Bacteroides fragilis
NCBI taxonomy ID ncbi_taxonomy_id	272559
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	528

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3cmgA01
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	3cmgA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3cmgA03
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	3cmgA04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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Unit-cell length a length_a	79.651 Å
Unit-cell length b length_b	102.878 Å
Unit-cell length c length_c	199.967 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	39.840 Å
R factor r_factor	0.1500
R_work r_work	0.1480
R_free r_free	0.1860

Crystal structure of putative beta-galactosidase from Bacteroides fragilis

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

Putative 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

3cmg__assembly_1__model_1

3cmg__assembly_1__model_1 | I(q)

3cmg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative beta-galactosidase from Bacteroides fragilis

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

Putative 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

3cmg__assembly_1__model_1

3cmg__assembly_1__model_1 | I(q)

3cmg__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

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) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)