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11yy

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

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	11yy
deposition_date	2026-03-19
last_revision	2026-04-29
title	E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo ACTGACTT
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	29.68 Å
i0	89853200.00
molecular_weight	72671.0 kDa
excluded_volume	90237 Å³
envelope_volume	117550 Å³
shell_volume	34163 Å³
envelope_diameter	102.2 Å
shell_rg	35.69 Å
envelope_rg	29.54 Å
shape_rg	29.70 Å
total_rg	30.17 Å
total_atoms	5105
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	30.13 Å
rg_real_error	0.96 Å
i0_real	8.9850e+07
i0_real_error	1.4520e+06
rg_reciprocal	30.10 Å
i0_reciprocal	89850000.0000
total_estimate	0.8810
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.7 Å
skewness	0.408
kurtosis	-0.295
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	15530000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.848; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.957; Smooth: 0.951

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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	72170.6 kDa
ec_number	5.6.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5213

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKK

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PAPCPTPGPAPCPTPT)-3') ;
formula_weight	2401.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

ACTGACTT

Entity 3 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	SUCCINIC ACID
formula_weight	118.1 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	MALONIC ACID
formula_weight	104.1 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	108

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6. Citations (1)

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length_a	109.912 Å
length_b	132.372 Å
length_c	78.777 Å
angle_alpha	90.00 °
angle_beta	134.24 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.200 Å
resolution_low	56.440 Å
r_factor	0.2176
r_work	0.2166
r_free	0.2357

fit	/app/data/saxs_computation/1y/11yy/11yy.fit
pddf	/app/data/pr_computation/1y/11yy/11yy.pr.out
profile	/app/data/saxs_computation/1y/11yy/11yy.dat

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

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 (1)

7. Files & Curves (10)

Files (7)

Curves (3)