SAXSdb — 1to3

▼

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

Putative aldolase yihT

Salmonella typhimurium

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	PHOSPHATE ION × 6 BROMIDE ION × 18 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YIHT_SALTY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–294； UniProt 2–292

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	1to3
Deposition date deposition_date	2004-06-11
Structure title title	Structure of yiht from Salmonella typhimurium
Keywords keywords	;beta-alpha barrel, Structural Genomics, PSI, Protein Structure Initiative, New York SGX Research Center for Structural Genomics, NYSGXRC, UNKNOWN FUNCTION ;; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

1to3__assembly_1__model_1

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

Download this curve (.dat)

1to3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1to3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.74 Å
Rg (electron density)	27.03 Å
Total Rg	27.36 Å
Atom count	4484
Residues	560
Excluded volume	80453 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1to3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Putative aldolase yihT
Molecular weight formula_weight	33813.0 kDa
EC 编号 ec_number	4.1.-.-
Mutation mutation	A289G
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	2362

MSLNNYTIKDITRASGGFAMLAVDQREAMRLMFAAAGAKTPVADSVLTDFKVNAAKILSPYASAVLLDQQFCYRQAVEQNAVAKSCAMIVAADDFIPGNGIPVDNVVLDKKINAQAVKRDGAKALKLLVLWRSDEDAQQRLNMVKEFNELCHSNGLLSIIEPVVRPPRCGDKFDREQAIIDAAKELGDSGADLYKVEMPLYGKGARSDLLTASQRLNGHINMPWVILSSGVDEKLFPRAVRVAMEAGASGFLAGRAVWSSVIGLPDTELMLRDVSAPKLQRLGEIVDEMMGKRREGGSHHHHHH

Source Source

Source organism organism	Salmonella typhimurium
NCBI taxonomy ID ncbi_taxonomy_id	602
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	3

Entity 3 Entity 3 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 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	120

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1to3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.10 — Aldolase
Family Family family	c.1.10.1 — Class I aldolase

Domain ID domain_id	d1to3a2
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 (1 domains)

Domain ID domain_id	1to3A00
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	70 — Aldolase class I

▶

Unit-cell length a length_a	141.144 Å
Unit-cell length b length_b	141.144 Å
Unit-cell length c length_c	102.726 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	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1802
R_work r_work	0.1787
R_free r_free	0.2082

Structure of yiht from Salmonella typhimurium

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

Putative aldolase yihT

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

1to3__assembly_1__model_1

1to3__assembly_1__model_1 | I(q)

1to3__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)

Structure of yiht from Salmonella typhimurium

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

Putative aldolase yihT

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

1to3__assembly_1__model_1

1to3__assembly_1__model_1 | I(q)

1to3__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) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

7. Citations (1)