SAXSdb — 9t56

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1. Structure Basics

entry_id	9t56
deposition_date	2025-11-04
title	Cryo-EM structure of ISCro4-DBL-TBL-tDNA-dDNA synaptic complex
keywords	Nucleic acid interaction, RNA binding, DNA binding, tetramer, recombination, recombinase; RECOMBINATION
method	ELECTRON MICROSCOPY

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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	37.35 Å
rg_electron	36.80 Å
i0	976958000.00
molecular_weight	206240.0 kDa
excluded_volume	237410 Å³
envelope_volume	323630 Å³
shell_volume	69401 Å³
envelope_diameter	112.7 Å
shell_rg	46.28 Å
envelope_rg	35.88 Å
shape_rg	36.83 Å
total_rg	37.16 Å
total_atoms	14212
n_residues	1461
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	111.2 Å
rg_real	37.01 Å
rg_real_error	0.81 Å
i0_real	9.7700e+08
i0_real_error	1.6010e+07
rg_reciprocal	37.23 Å
i0_reciprocal	977200000.0000
total_estimate	0.8993
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	50.3 Å
skewness	-0.015
kurtosis	-0.557
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0000
highest_alpha	80610000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.954

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	ISCro4 transposase
formula_weight	38131.7 kDa
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	14212

SNAMEQELHFIGIDVSKAKLDVDVLRPDGRHRSKKFANTPKGHDELLRWLSGHRVAPAHICMEATSTYMEDVAAHLSDAGYTVSVINPALGKAFAQSEGLRSKTDAVDARMLAEFCRQKRPPAWEAPHPVERALRALVLRHQSLTDMHTQELNRLETAREVQRPSIDAHLLWLHAELKRIEKQIKDLTDDDPDMKHRRKLLESIPGIGEKTSAVLLAYTGLKERFTHARQFAAFAGLTPRRYESGSSVNRASRMSKAGHASLRRALYMPAMVAVSKTEWGRAFRDRLAGNGKKGKVIIGAMMRKLAQVAYGVLKSGVPFDASRHNPVAASSGSLEHHHHHH

Source

organism	Citrobacter rodentium ICC168
ncbi_taxonomy_id	637910
host_organism	Escherichia coli

Entity 2 polymer

description	Target-binding loop (TBL) RNA
formula_weight	35682.1 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	E

GGGAGUGCAGGGAGAACCGGCCAGUUCUCUCUGCCAUGCGGUCCGCAUGCCGUAUCAGGCCUCAGGCUAAUAACCUGUGACGUAGAUUUAUGCAGCGGACCGCCGUUUUUU

Entity 3 polymer

description	Donor-binding loop (DBL) RNA
formula_weight	25278.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	F

GGGCAAGUGACAAACCGGACAGUAUCAUGGACCGGUUUUCCCGGUAAUCCGCAUUCACAAGGCUGGUCUCACUUUUUUU

Entity 4 polymer

description	target DNA (tRNA) top strand
formula_weight	11616.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	G

GCCGGGTAATACCCTTATCAGGCCTACGTCACAGCTCG

Entity 5 polymer

description	target DNA (tDNA) bottom strand
formula_weight	11776.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	H

CGAGCTGTGACGTAGGCCTGATAAGGGTATTACCCGGC

Entity 6 polymer

description	donor DNA (dDNA) top strand
formula_weight	13562.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	I

TGCAGGCGATAACAGTATCTTGTATTATCCCTTCAGTGCAGAGA

Entity 7 polymer

description	donor DNA (dDNA) bottom strand
formula_weight	13531.7 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	J

TCTCTGCACTGAAGGGATAATACAAGATACTGTTATCGCCTGCA

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

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6. Citations (1)

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length_a	1.000 Å
length_b	1.000 Å
length_c	1.000 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	—

space_group	P 1
int_tables_number	1
crystal_system	—

resolution	2.810 Å
resolution_low	— Å
r_factor	—
r_work	—
r_free	—

resolution	2.81 Å
resolution_method	—
num_particles	268987

fit	/app/data/saxs_computation/t5/9t56/9t56.fit
pddf	/app/data/pr_computation/t5/9t56/9t56.pr.out
profile	/app/data/saxs_computation/t5/9t56/9t56.dat

Cryo-EM structure of ISCro4-DBL-TBL-tDNA-dDNA synaptic complex

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

EM 3D

5. Entities & Polymer Info (8)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 polymer

Polymer

Entity 6 polymer

Polymer

Entity 7 polymer

Polymer

Entity 8 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)