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11kb

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

Method: X-RAY DIFFRACTION D_max: 102.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11kb
deposition_date	2026-02-27
last_revision	2026-04-29
title	E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo AACTGTTG
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	30.25 Å
rg_electron	29.81 Å
i0	86503300.00
molecular_weight	71947.0 kDa
excluded_volume	89635 Å³
envelope_volume	117540 Å³
shell_volume	34085 Å³
envelope_diameter	103.3 Å
shell_rg	35.69 Å
envelope_rg	29.62 Å
shape_rg	29.82 Å
total_rg	30.33 Å
total_atoms	5060
n_residues	625
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	102.5 Å
rg_real	30.31 Å
rg_real_error	0.77 Å
i0_real	8.6500e+07
i0_real_error	1.4150e+06
rg_reciprocal	30.28 Å
i0_reciprocal	86500000.0000
total_estimate	0.8788
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.5 Å
skewness	0.399
kurtosis	-0.287
angular_range	— – 0.2600 Å⁻¹
current_alpha	0.0000
highest_alpha	15910000.0000
n_real_points	53
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.907

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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

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	5542

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKENLYFQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(CPGPCPAPAPCPTPT)-3') ;
formula_weight	2441.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

AACTGTTG

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

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

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	401

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6. Citations (2)

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length_a	38.966 Å
length_b	123.124 Å
length_c	86.255 Å
angle_alpha	90.00 °
angle_beta	98.67 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.900 Å
resolution_low	42.640 Å
r_factor	0.1907
r_work	0.1888
r_free	0.2281

fit	/app/data/saxs_computation/1k/11kb/11kb.fit
pddf	/app/data/pr_computation/1k/11kb/11kb.pr.out
profile	/app/data/saxs_computation/1k/11kb/11kb.dat

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

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 (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)