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9t38

Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu

Method: X-RAY DIFFRACTION D_max: 125.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9t38
deposition_date	2025-10-27
last_revision	2025-12-24
title	Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu
keywords	T6SS, effector-immunity compex, HNH endonuclease, DNAse, S. marcescens DB10, ANTIMICROBIAL PROTEIN, EF-Tu; ANTIMICROBIAL PROTEIN
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	37.90 Å
rg_electron	38.04 Å
i0	330579000.00
molecular_weight	146930.0 kDa
excluded_volume	183880 Å³
envelope_volume	242790 Å³
shell_volume	54543 Å³
envelope_diameter	137.3 Å
shell_rg	42.62 Å
envelope_rg	37.57 Å
shape_rg	38.05 Å
total_rg	38.28 Å
total_atoms	10341
n_residues	1313
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	125.9 Å
rg_real	37.98 Å
rg_real_error	1.27 Å
i0_real	3.3060e+08
i0_real_error	5.6350e+06
rg_reciprocal	37.93 Å
i0_reciprocal	330600000.0000
total_estimate	0.8729
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	42.0 Å
skewness	0.416
kurtosis	-0.238
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	44850000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.870; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.736

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	Elongation factor Tu 2
formula_weight	43370.5 kDa
ec_number	3.6.5.3
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F
atom_count	10491

MSKEKFERTKPHVNVGTIGHVDHGKTTLTAAITTVLAKTYGGAARAFDQIDNAPEEKARGITINTSHVEYDTPTRHYAHVDCPGHADYVKNMITGAAQMDGAILVVAATDGPMPQTREHILLGRQVGVPYIIVFLNKCDMVDDEELLELVEMEVRELLSQYDFPGDDTPIVRGSALKALEGDAEWEAKILELAGFLDSYIPEPERAIDKPFLLPIEDVFSISGRGTVVTGRVERGIIKVGEEVEIVGIKETQKSTCTGVEMFRKLLDEGRAGENVGVLLRGIKREEIERGQVLAKPGTIKPHTKFESEVYILSKDEGGRHTPFFKGYRPQFYFRTTDVTGTIELPEGVEMVMPGDNIKMVVTLIHPIAMDDGLRFAIREGGRTVGAGVVAKVLS

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	Immunity protein RhsI2
formula_weight	18682.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MNEFDFDSLLQRIDSSCFFSRMGLPDVLDSRVILIENVEKVFVNPTDAEFKGYYDSVEWLPTSMTQEDPFYKVKEVLPKELTGLRIRVNKAVMNATKGLSKDKFNYGPHDFSLAARNGICFAFREYVSEQYLHLGNKWEEVVGIYFSGHWPVGIAKDKIVTI

Source

organism	Serratia marcescens
ncbi_taxonomy_id	615
host_organism	Escherichia coli BL21(DE3)

Entity 3 polymer

description	Rhs-family protein
formula_weight	17797.0 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D

MGSSHHHHHHSSGENLYFQGGSNCSTLDRIIGDANKVASRGGAITAKQAQILRDNLPVVQRRSVFQNQMARKEFVRDQHYLMSQWEANTGRTWPTGATPHHIIPLESGGANKWWNLMPTHGTLPNHSLPGVPGPHAAGGVLRTTVQQSRKALPPGTITDLRL

Source

organism	Serratia marcescens
ncbi_taxonomy_id	615
host_organism	Escherichia coli BL21(DE3)

Entity 4 non-polymer

description	GUANOSINE-5'-DIPHOSPHATE
formula_weight	443.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	nat
entity_count	2

Entity 7 non-polymer

description	IMIDAZOLE
formula_weight	69.1 kDa
src_method	nat
entity_count	2

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	146

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6. Citations (1)

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length_a	61.598 Å
length_b	110.569 Å
length_c	113.863 Å
angle_alpha	90.00 °
angle_beta	102.39 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.450 Å
resolution_low	60.236 Å
r_factor	—
r_work	0.2704
r_free	0.3138

fit	/app/data/saxs_computation/t3/9t38/9t38.fit
pddf	/app/data/pr_computation/t3/9t38/9t38.pr.out
profile	/app/data/saxs_computation/t3/9t38/9t38.dat

Rhs2-CT endonuclease toxin in complex with cognate immunity protein RhsI2 and EF-Tu

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)