3fn9

Crystal structure of putative beta-galactosidase from bacteroides fragilis

Method: X-RAY DIFFRACTION

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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 3	CHLORIDE ION × 6 water × 3	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	CHLORIDE ION × 7 water × 3	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	CHLORIDE ION × 13 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LJ68_BACFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–684； UniProt 23–703 Author chain B； PDBConstruct 4–684； UniProt 23–703 Author chain C； PDBConstruct 4–684； UniProt 23–703 Author chain D； PDBConstruct 4–684； UniProt 23–703

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	3fn9
Deposition date deposition_date	2008-12-23
Structure title title	Crystal structure of putative beta-galactosidase from bacteroides fragilis
Keywords keywords	;structural genomics, Putative beta-galactosidase, Glycosidase, Hydrolase, PSI-2, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC ;; 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.

3fn9__assembly_1__model_1

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

Download this curve (.dat)

3fn9__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3fn9__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	47.33 Å
Rg (electron density)	47.23 Å
Total Rg	47.18 Å
Atom count	16216
Residues	2010
Excluded volume	286780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3fn9__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3fn9__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3fn9__assembly_3__model_1`	hexameric （6）	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 (3)

Entity 1 Entity 1 polymer

Description description	Putative beta-galactosidase
Molecular weight formula_weight	79344.9 kDa
EC 编号 ec_number	3.2.1.23
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	21740

MSLARQVTAFNTGWQFKKGPFATDPMRAASQWDGKWETVEIPHTWNAMDMQVQSGSFYEGAGYYRKTQFFPHDLEGKRVFLRFEGVGACAEVYVNGKLAGTHKGGYSAFACEIGTALKLGAENEIIVKADNKARPDVIPVNQNLFGVYGGIYRPVWLIVTEQNNITVTDCASPGVYITQKDVSKKSADITVKVKLDNAGLQPAAVTLENTIYTQEGQKVGTHSRSFDLSPQGTQTYLSTFKLKNPHLWQGRKDPYLYKVVCRLMADGKVIDEVVQPLGVRKYEIVAGKGFFLNGEKYSMYGVTRHQDWWGLGSALKNEHHDFDLAAIMDVGATTVRFAHYQQSDYLYSRCDTLGLIIWAEIPCVNRVTGYETENAQSQLRELIRQSFNHPSIYVWGLHNEVYQPHEYTAALTRSLHDLAKTEDPDRYTVSVNGYGHMDHPVNLNADIQGMNRYFGWYEKKIQDIKPWVEQLEKDYPYQKLMLTEYGADANLAHQTEYLGDALNWGKPFYPETFQTKTHEYQWSIIKDHPYIIASYLWNMFDFAVPMWTRGGVPARNMKGLITFDRKTKKDSYFWYKANWSEEPVLYLTQRRNADREKRTTAVTVYSNIGTPKVYLNGQELSGIRNGYTDVHYVFDNVSLADGKNILKAVVSTKGKEYTDEIEWNYSGEKNREIDSYENKNEHSGEGHHHHHH

Source Source

Source organism organism	Bacteroides fragilis
NCBI taxonomy ID ncbi_taxonomy_id	272559
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	92

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6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

Domain ID domain_id	3fn9A01
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	3fn9A02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9A03
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	3fn9A04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9B01
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	3fn9B02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9B03
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	3fn9B04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9C01
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	3fn9C02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9C03
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	3fn9C04
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9D01
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	3fn9D02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	3fn9D03
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	3fn9D04
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	109.453 Å
Unit-cell length b length_b	133.066 Å
Unit-cell length c length_c	221.192 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	16

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

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	49.390 Å
R factor r_factor	0.2040
R_work r_work	0.2010
R_free r_free	0.2700

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

3fn9__assembly_1__model_1

3fn9__assembly_1__model_1 | I(q)

3fn9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 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

3fn9__assembly_1__model_1

3fn9__assembly_1__model_1 | I(q)

3fn9__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

CATH v4.4 (16 domains)

7. Citations (1)