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11gx

E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CGCAACTT

Method: X-RAY DIFFRACTION D_max: 101.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11gx
deposition_date	2026-02-23
last_revision	2026-04-29
title	E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CGCAACTT
keywords	EcTopo3, ssDNA complex, ISOMERASE, ISOMERASE-DNA complex; ISOMERASE/DNA
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	30.06 Å
rg_electron	29.71 Å
i0	88411700.00
molecular_weight	72309.0 kDa
excluded_volume	89897 Å³
envelope_volume	117820 Å³
shell_volume	34232 Å³
envelope_diameter	102.4 Å
shell_rg	35.66 Å
envelope_rg	29.64 Å
shape_rg	29.73 Å
total_rg	30.19 Å
total_atoms	5083
n_residues	628
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	101.9 Å
rg_real	30.14 Å
rg_real_error	1.04 Å
i0_real	8.8410e+07
i0_real_error	1.5230e+06
rg_reciprocal	30.10 Å
i0_reciprocal	88410000.0000
total_estimate	0.8761
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.7 Å
skewness	0.427
kurtosis	-0.254
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	17130000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.912

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	DNA topoisomerase 3
formula_weight	72965.4 kDa
ec_number	5.6.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5143

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKENLYFQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(CPGPCPAPAPCPTPT)-3') ;
formula_weight	2386.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

CGCAACTT

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	60

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6. Citations (2)

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length_a	111.385 Å
length_b	132.520 Å
length_c	77.321 Å
angle_alpha	90.00 °
angle_beta	133.96 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.220 Å
resolution_low	42.620 Å
r_factor	0.2224
r_work	0.2205
r_free	0.2605

fit	/app/data/saxs_computation/1g/11gx/11gx.fit
pddf	/app/data/pr_computation/1g/11gx/11gx.pr.out
profile	/app/data/saxs_computation/1g/11gx/11gx.dat

E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CGCAACTT

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)