2afa

Crystal Structure of putative NAG isomerase from Salmonella typhimurium

Method: X-RAY DIFFRACTION

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

NAG isomerase

Salmonella typhimurium

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q8ZKT7_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–415； UniProt 2–413 Author chain B； PDBConstruct 4–415； UniProt 2–413 Author chain C； PDBConstruct 4–415； UniProt 2–413 Author chain D； PDBConstruct 4–415； UniProt 2–413 Author chain E； PDBConstruct 4–415； UniProt 2–413 Author chain F； PDBConstruct 4–415； UniProt 2–413

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2afa
Deposition date deposition_date	2005-07-25
Structure title title	Crystal Structure of putative NAG isomerase from Salmonella typhimurium
Keywords keywords	;NAG isomerase, Dimer-of-Trimers, renin-binding protein, alpha/alpha-fold, T1489, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, ISOMERASE ;; 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.

2afa__assembly_1__model_1

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

Download this curve (.dat)

2afa__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2afa__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	41.01 Å
Rg (electron density)	39.93 Å
Total Rg	40.23 Å
Atom count	19908
Residues	2394
Excluded volume	351390 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2afa__assembly_1__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 (2)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d2afaa1
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	d2afaa2
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	d2afab2
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	d2afab3
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	d2afac2
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	d2afac3
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	d2afad2
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	d2afad3
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	d2afae2
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	d2afae3
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	d2afaf2
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	d2afaf3
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	2afaA00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2afaB00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2afaC00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2afaD00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2afaE00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2afaF00
Class class	1 — Mainly Alpha
Architecture architecture	50 — Alpha/alpha barrel
Topology topology	10 — Glycosyltransferase
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	88.933 Å
Unit-cell length b length_b	91.140 Å
Unit-cell length c length_c	95.102 Å
Unit-cell angle α angle_alpha	106.81 °
Unit-cell angle β angle_beta	103.52 °
Unit-cell angle γ angle_gamma	111.79 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	2.150 Å
Low-resolution limit resolution_low	45.770 Å
R factor r_factor	0.2070
R_work r_work	0.2070
R_free r_free	0.2460

Description description	NAG isomerase
Molecular weight formula_weight	49413.8 kDa
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	20569

Crystal Structure of putative NAG isomerase from Salmonella typhimurium

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

NAG 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

2afa__assembly_1__model_1

2afa__assembly_1__model_1 | I(q)

2afa__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
Host organism host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	661

Crystal Structure of putative NAG isomerase from Salmonella typhimurium

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

NAG 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

2afa__assembly_1__model_1

2afa__assembly_1__model_1 | I(q)

2afa__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (12 domains)

CATH v4.4 (6 domains)

7. Citations (1)