7ag4

Crystal structure of active site mutant of SQ Isomerase (YihS-H248A) from Salmonella enterica in complex with sulfofructose (SF)

Method: X-RAY DIFFRACTION

▼

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

Sulfoquinovose isomerase

Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	6-deoxy-6-sulfo-D-fructose × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SQUS_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–433； UniProt 1–413 Author chain B； PDBConstruct 21–433； UniProt 1–413 Author chain C； PDBConstruct 21–433； UniProt 1–413 Author chain D； PDBConstruct 21–433； UniProt 1–413 Author chain E； PDBConstruct 21–433； UniProt 1–413 Author chain F； PDBConstruct 21–433； UniProt 1–413

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	7ag4
Deposition date deposition_date	2020-09-21
Structure title title	Crystal structure of active site mutant of SQ Isomerase (YihS-H248A) from Salmonella enterica in complex with sulfofructose (SF)
Keywords keywords	sulfofructose, sulfoquinovose, SQ isomerase, sulfoglycolysis, ISOMERASE; ISOMERASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

7ag4__assembly_1__model_1

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

Download this curve (.dat)

7ag4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7ag4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	40.56 Å
Rg (electron density)	39.52 Å
Total Rg	39.86 Å
Atom count	20027
Residues	2502
Excluded volume	352480 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7ag4__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Sulfoquinovose isomerase
Molecular weight formula_weight	49689.7 kDa
EC 编号 ec_number	5.3.1.31
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,D,F,C,E
Atom count atom_count	20713

MGSSHHHHHHSSGLVPRGSHMKWFNTLSHNRWLEQETDRIFNFGKNAVVPTGFGWLGNKGQIKEEMGTHLWITARMLHVYSVAASMGRPGAYDLVDHGIKAMNGALRDKKYGGWYACVNDQGVVDASKQGYQHFFALLGAASAVTTGHPEARKLLDYTIEVIEKYFWSEEEQMCLESWDEAFSQTEDYRGGNANMHAVEAFLIVYDVTHDKKWLDRALRIASVIIHDVARNGDYRVNEHFDSQWNPIRDYNKDNPAHRFRAYGGTPGAWIEWGRLMLHLHAALEARFETPPAWLLEDAKGLFHATIRDAWAPDGADGFVYSVDWDGKPIVRERVRWPIVEAMGTAYALYTLTDDSQYEEWYQKWWDYCIKYLMDYENGSWWQELDADNKVTTKVWDGKQDIYHLLHCLVIPRLPLAPGLAPAVAAGLLDINAK

Source Source

Source organism organism	Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
NCBI taxonomy ID ncbi_taxonomy_id	99287
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	6-deoxy-6-sulfo-D-fructose
Molecular weight formula_weight	244.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	686

▼

6. Fold Classification (SCOP + CATH) 17 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d7ag4a_
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
Family Family family	a.102.1.3 — N-acylglucosamine (NAG) epimerase

Domain ID domain_id	d7ag4b1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
Family Family family	a.102.1.3 — N-acylglucosamine (NAG) epimerase

Domain ID domain_id	d7ag4b2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7ag4c1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
Family Family family	a.102.1.3 — N-acylglucosamine (NAG) epimerase

Domain ID domain_id	d7ag4c2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7ag4d1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
Family Family family	a.102.1.3 — N-acylglucosamine (NAG) epimerase

Domain ID domain_id	d7ag4d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7ag4e1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
Family Family family	a.102.1.3 — N-acylglucosamine (NAG) epimerase

Domain ID domain_id	d7ag4e2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d7ag4f1
Class class	a — All alpha proteins
Fold Fold fold	a.102 — alpha/alpha toroid
Superfamily Superfamily superfamily	a.102.1 — Six-hairpin glycosidases
Family Family family	a.102.1.3 — N-acylglucosamine (NAG) epimerase

Domain ID domain_id	d7ag4f2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id	7ag4A01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7ag4B01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7ag4C01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7ag4D01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7ag4E01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	7ag4F01
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	87.818 Å
Unit-cell length b length_b	136.827 Å
Unit-cell length c length_c	230.036 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.35 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

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

Resolution resolution	2.130 Å
Low-resolution limit resolution_low	52.010 Å
R factor r_factor	0.1815
R_work r_work	0.1805
R_free r_free	0.2008

Crystal structure of active site mutant of SQ Isomerase (YihS-H248A) from Salmonella enterica in complex with sulfofructose (SF)

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

Sulfoquinovose isomerase

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

7ag4__assembly_1__model_1

7ag4__assembly_1__model_1 | I(q)

7ag4__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) 17 domains

SCOP 2.08 (11 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of active site mutant of SQ Isomerase (YihS-H248A) from Salmonella enterica in complex with sulfofructose (SF)

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

Sulfoquinovose isomerase

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

7ag4__assembly_1__model_1

7ag4__assembly_1__model_1 | I(q)

7ag4__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) 17 domains

SCOP 2.08 (11 domains)

CATH v4.4 (6 domains)

7. Citations (1)