SAXSdb — 9vxg

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

UPF0225 protein YchJ

Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YCHJ_SALTY
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 2–131； UniProt 1–130 Author chain B； PDBConstruct 1–16； UniProt 133–148

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	9vxg
Deposition date deposition_date	2025-07-18
Last revision last_revision	2025-08-06
Structure title title	ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages
Keywords keywords	DNA binding, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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.

9vxg__assembly_1__model_1

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

Download this curve (.dat)

9vxg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9vxg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	16.77 Å
Rg (electron density)	15.69 Å
Total Rg	16.82 Å
Atom count	1162
Residues	147
Excluded volume	20452 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9vxg__assembly_1__model_1`	dimeric （2）	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	UPF0225 protein YchJ
Molecular weight formula_weight	14874.8 kDa
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	1182

KMSQPCPCGSADEYSLCCGRIVSGERVAPDPSHLMRSRYCAFVMKDADYLIKSWHPTCNAAAFRDDIIAGFANTRWLGLTIFEHTWSEAENTGYVSFIARFSEQGKNGAIIERSRFIKENGQWYYIDGTRP

Source Source

Source organism organism	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NCBI taxonomy ID ncbi_taxonomy_id	588858
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	UPF0225 protein YchJ
Molecular weight formula_weight	1727.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GRNDPCPCGSGKKFKK

Source Source

Source organism organism	Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
NCBI taxonomy ID ncbi_taxonomy_id	588858
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	20

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Unit-cell length a length_a	58.937 Å
Unit-cell length b length_b	58.937 Å
Unit-cell length c length_c	124.367 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	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.302 Å
Low-resolution limit resolution_low	29.468 Å
R factor r_factor	0.2333
R_work r_work	0.2316
R_free r_free	0.2662

ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages

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

UPF0225 protein YchJ

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

9vxg__assembly_1__model_1

9vxg__assembly_1__model_1 | I(q)

9vxg__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

ROS-Sensing Transcription Factor YchJ Regulates the RssB-RpoS Pathway to Protect Salmonella Against Oxidative Attack by Macrophages

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

UPF0225 protein YchJ

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

9vxg__assembly_1__model_1

9vxg__assembly_1__model_1 | I(q)

9vxg__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 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)