SAXSdb — 8s2m

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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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–134	Not recorded	Complete genome segment 11/17 × 1 （D3UXR3）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0,5 % v/v Jeffamine ED-2003	Resolution 1.28 Å R-free 0.185

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8S2M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8S2N Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein Deposited 2024-02-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–134（134 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.02 M Sodium chloride, 0.02 M Sodium acetate pH 4.0, 33 % v/v PEG 200	Resolution 2.11 Å R-free 0.232
9GCO Xenorhabdus bovienii Thioredoxin complex with Rhs toxin TreX and immunity protein TriX Deposited 2024-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–134（134 aa）	Not recorded	CA CALCIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium chloride dihydrate, 0.1 M Tris-HCl pH 8.0, 44 % v/v PEG 400	Resolution 2.00 Å R-free 0.223
9GCO Xenorhabdus bovienii Thioredoxin complex with Rhs toxin TreX and immunity protein TriX Deposited 2024-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–134（134 aa）	Not recorded	CA CALCIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium chloride dihydrate, 0.1 M Tris-HCl pH 8.0, 44 % v/v PEG 400	Resolution 2.00 Å R-free 0.223

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1380–1518	Not recorded	Immunity Protein TriX × 1 （D3UXR2）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；1.1 M Sodium malonate dibasic monohydrate, 0.1 M HEPES pH 7.0, 0,5 % v/v Jeffamine ED-2003	Resolution 1.28 Å R-free 0.185

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 8S2M	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8S2N Xenorhabdus bovienii Rhs toxin TreTu complex with TrxA and TriTu immunity protein Deposited 2024-02-18	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1380–1518（139 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 3 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Ammonium sulfate, 0.02 M Sodium chloride, 0.02 M Sodium acetate pH 4.0, 33 % v/v PEG 200	Resolution 2.11 Å R-free 0.232
9GCO Xenorhabdus bovienii Thioredoxin complex with Rhs toxin TreX and immunity protein TriX Deposited 2024-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1380–1518（139 aa）	Not recorded	CA CALCIUM ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium chloride dihydrate, 0.1 M Tris-HCl pH 8.0, 44 % v/v PEG 400	Resolution 2.00 Å R-free 0.223
9GCO Xenorhabdus bovienii Thioredoxin complex with Rhs toxin TreX and immunity protein TriX Deposited 2024-08-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1380–1518（139 aa）	Not recorded	CA CALCIUM ION × 3 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Calcium chloride dihydrate, 0.1 M Tris-HCl pH 8.0, 44 % v/v PEG 400	Resolution 2.00 Å R-free 0.223

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

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

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	8s2m
Deposition date deposition_date	2024-02-18
Structure title title	Xenorhabdus bovienii Rhs C-terminal toxin TreX complex with TriX immunity protein
Keywords keywords	ADP-ribosyltransferase, TOXIN; TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	19.06 Å
Radius of gyration Rg (electron density) rg_electron	18.40 Å
Forward intensity I(0) i0	15618900.00
Molecular weight molecular_weight	29421.0 kDa
Excluded volume excluded_volume	36609 Å³
Envelope volume envelope_volume	41753 Å³
Hydration-shell volume shell_volume	18964 Å³
Envelope diameter envelope_diameter	66.7 Å
Shell Rg shell_rg	24.74 Å
Envelope Rg envelope_rg	18.78 Å
Shape Rg shape_rg	18.40 Å
Total Rg total_rg	19.32 Å
Total atoms total_atoms	2070
Residues n_residues	260
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.7 Å
Rg (real space) rg_real	19.02 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.5620e+07
I(0) uncertainty (real space) i0_real_error	1.9460e+05
Rg (reciprocal space) rg_reciprocal	19.02 Å
I(0) (reciprocal space) i0_reciprocal	15620000.0000
Solution quality estimate total_estimate	0.8590
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.346
Kurtosis Kurtosis kurtosis	-0.186
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5388000.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.743; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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	2401

MTDVDKRKIKIILNGEMEEAELHMITSPNRHCCLKIFHNNNQLAESNDTDYFSCFADLRNQLKNIIFLCKGAKINVYPSAMSRDMSDGIVAYETTLGQPGLPENQVHIFDFEDKYVDITPEEQRKFHSQWFESLVDHHHHHH

来源 Source

来源生物 organism	Xenorhabdus bovienii SS-2004
NCBI Class编号 ncbi_taxonomy_id	406818
宿主生物 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

来源 Source

来源生物 organism	Xenorhabdus bovienii SS-2004
NCBI Class编号 ncbi_taxonomy_id	406818
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	282

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8. Citations (1)

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Unit-cell length a length_a	77.995 Å
Unit-cell length b length_b	93.855 Å
Unit-cell length c length_c	39.903 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	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	orthorhombic

Resolution resolution	1.280 Å
Low-resolution limit resolution_low	40.210 Å
R factor r_factor	0.1711
R_work r_work	0.1707
R_free r_free	0.1849

fit	/app/data/saxs_computation/s2/8s2m/8s2m.fit
pddf	/app/data/pr_computation/s2/8s2m/8s2m.pr.out
profile	/app/data/saxs_computation/s2/8s2m/8s2m.dat

Xenorhabdus bovienii Rhs C-terminal toxin TreX complex with TriX 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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)