SAXSdb — 3etn

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

putative phosphosugar isomerase involved in capsule formation

Bacteroides fragilis NCTC 9343

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	;CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID ; × 4 1,2-ETHANEDIOL × 9 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q5LIW1_BACFN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–220； UniProt 1–201 Author chain B； PDBConstruct 20–220； UniProt 1–201 Author chain C； PDBConstruct 20–220； UniProt 1–201 Author chain D； PDBConstruct 20–220； UniProt 1–201

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	3etn
Deposition date deposition_date	2008-10-08
Structure title title	Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution
Keywords keywords	;YP_209877.1, putative phosphosugar isomerase involved in capsule formation, Structural Genomics, Joint Center for Structural Genomics, JCSG, Protein Structure Initiative, PSI-2, Isomerase, Unknown function ;; ISOMERASE
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.

3etn__assembly_1__model_1

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

Download this curve (.dat)

3etn__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3etn__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.79 Å
Rg (electron density)	24.85 Å
Total Rg	25.57 Å
Atom count	6051
Residues	756
Excluded volume	108790 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3etn__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 (4)

Entity 1 Entity 1 polymer

Description description	putative phosphosugar isomerase involved in capsule formation
Molecular weight formula_weight	24477.0 kDa
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	7088

MGSDKIHHHHHHENLYFQGMIESIQELLQKEAQAVLNIPVTDAYEKAVELIVEQIHRKKGKLVTSGMGKAGQIAMNIATTFCSTGIPSVFLHPSEAQHGDLGILQENDLLLLISNSGKTREIVELTQLAHNLNPGLKFIVITGNPDSPLASESDVCLSTGHPAEVCTLGMTPTTSTTVMTVIGDILVVQTMKRTEFTIEEYSKRHHGGYLGEKSRKLCVK

Source Source

Source organism organism	Bacteroides fragilis NCTC 9343
NCBI taxonomy ID ncbi_taxonomy_id	272559
Host organism host_organism	Escherichia Coli

Entity 2 Entity 2 non-polymer

Description description	;CYTIDINE 5'-MONOPHOSPHATE 3-DEOXY-BETA-D-GULO-OCT-2-ULO-PYRANOSONIC ACID ;
Molecular weight formula_weight	543.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	725

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	3etnA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	3etnB00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	3etnC00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

Domain ID domain_id	3etnD00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10490 — Glucose-6-phosphate isomerase like protein; domain 1

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Unit-cell length a length_a	60.409 Å
Unit-cell length b length_b	114.267 Å
Unit-cell length c length_c	115.917 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	1.700 Å
Low-resolution limit resolution_low	29.223 Å
R factor r_factor	0.1730
R_work r_work	0.1720
R_free r_free	0.1970

Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution

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

putative phosphosugar isomerase involved in capsule formation

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

3etn__assembly_1__model_1

3etn__assembly_1__model_1 | I(q)

3etn__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Crystal structure of putative phosphosugar isomerase involved in capsule formation (YP_209877.1) from Bacteroides fragilis NCTC 9343 at 1.70 A resolution

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

putative phosphosugar isomerase involved in capsule formation

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

3etn__assembly_1__model_1

3etn__assembly_1__model_1 | I(q)

3etn__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 (4)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)