SAXSdb — 8s2n

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

Immunity Protein TriX

Xenorhabdus bovienii SS-2004

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Complete genome segment 11/17 × 1 （D3UXR3） Thioredoxin 1 × 1 （P0AA25） DI(HYDROXYETHYL)ETHER × 3 SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3UXR2_XENBS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–134； UniProt 1–134

Complete genome segment 11/17

Xenorhabdus bovienii SS-2004

UniProt D3UXR3

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Immunity Protein TriX × 1 （D3UXR2） Thioredoxin 1 × 1 （P0AA25） DI(HYDROXYETHYL)ETHER × 3 SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	D3UXR3_XENBS
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 2–140； UniProt 1380–1518

Thioredoxin 1

Escherichia coli str. K-12 substr. MG1655

UniProt P0AA25

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Immunity Protein TriX × 1 （D3UXR2） Complete genome segment 11/17 × 1 （D3UXR3） DI(HYDROXYETHYL)ETHER × 3 SULFATE ION × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	THIO_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 4–111； UniProt 2–109

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	8s2n
Deposition date deposition_date	2024-02-18
Structure title title	Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein
Keywords keywords	ADP-ribosyltransferase, thioredoxin, TOXIN; TOXIN
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.

8s2n__assembly_1__model_1

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

Download this curve (.dat)

8s2n__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8s2n__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	24.88 Å
Rg (electron density)	24.65 Å
Total Rg	25.35 Å
Atom count	2953
Residues	372
Excluded volume	52552 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8s2n__assembly_1__model_1`	trimeric （3）	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 (6)

Entity 1 Entity 1 polymer

Description description	Immunity Protein TriX
Molecular weight formula_weight	16638.7 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	3019

MTDVDKRKIKIILNGEMEEAELHMITSPNRHCCLKIFHNNNQLAESNDTDYFSCFADLRNQLKNIIFLCKGAKINVYPSAMSRDMSDGIVAYETTLGQPGLPENQVHIFDFEDKYVDITPEEQRKFHSQWFESLVDHHHHHH

Source Source

Source organism organism	Xenorhabdus bovienii SS-2004
NCBI taxonomy ID ncbi_taxonomy_id	406818
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Complete genome segment 11/17
Molecular weight formula_weight	15317.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAGGIGNKGDYIITYRGDTRSFTEIFDKGFETLGPSKDLYKHALDNRAPPSDFVSTTIDPTKTISFATKYGQKSGYMYTMKTNHGIDVNKALGARSPFAAEAEIAMPGGVRAEDILGARAVNADGEMWDYTILNPKRYGK

Source Source

Source organism organism	Xenorhabdus bovienii SS-2004
NCBI taxonomy ID ncbi_taxonomy_id	406818
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Thioredoxin 1
Molecular weight formula_weight	11902.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

GASSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

Source Source

Source organism organism	Escherichia coli str. K-12 substr. MG1655
NCBI taxonomy ID ncbi_taxonomy_id	511145
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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Unit-cell length a length_a	74.600 Å
Unit-cell length b length_b	74.600 Å
Unit-cell length c length_c	190.703 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 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	2.110 Å
Low-resolution limit resolution_low	48.380 Å
R factor r_factor	0.1997
R_work r_work	0.1975
R_free r_free	0.2324

Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein

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

Immunity Protein TriX

State in the Current Structure

Other States of the Same Protein in the Database

Complete genome segment 11/17

State in the Current Structure

Other States of the Same Protein in the Database

Thioredoxin 1

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

8s2n__assembly_1__model_1

8s2n__assembly_1__model_1 | I(q)

8s2n__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)

Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein

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

Immunity Protein TriX

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Complete genome segment 11/17

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Thioredoxin 1

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

8s2n__assembly_1__model_1

8s2n__assembly_1__model_1 | I(q)

8s2n__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Citations (1)