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11lb

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

Method: X-RAY DIFFRACTION D_max: 100.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11lb
deposition_date	2026-03-02
last_revision	2026-04-29
title	E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo GCAACTGG
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	30.09 Å
rg_electron	29.64 Å
i0	89826700.00
molecular_weight	73054.0 kDa
excluded_volume	90904 Å³
envelope_volume	117860 Å³
shell_volume	34283 Å³
envelope_diameter	101.4 Å
shell_rg	35.62 Å
envelope_rg	29.45 Å
shape_rg	29.66 Å
total_rg	30.15 Å
total_atoms	5133
n_residues	626
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	100.8 Å
rg_real	30.14 Å
rg_real_error	0.68 Å
i0_real	8.9830e+07
i0_real_error	1.3290e+06
rg_reciprocal	30.12 Å
i0_reciprocal	89830000.0000
total_estimate	0.6640
solution_quality	REASONABLE a REASONABLE solution
n_peaks	1
r_peak_primary	34.2 Å
skewness	0.392
kurtosis	-0.298
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0002
highest_alpha	16580000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 0.050; Positv: 1.000; Valcen: 0.970; Smooth: 0.893

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

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	5521

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKENLYFQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(PAPAPCPTPGPG)-3') ;
formula_weight	2451.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GCAACTGG

Entity 3 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	8

Entity 4 non-polymer

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

Entity 5 non-polymer

description	CITRATE ANION
formula_weight	189.1 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	355

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6. Citations (1)

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length_a	38.685 Å
length_b	120.884 Å
length_c	85.609 Å
angle_alpha	90.00 °
angle_beta	99.34 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.850 Å
resolution_low	60.440 Å
r_factor	0.1795
r_work	0.1778
r_free	0.2118

fit	/app/data/saxs_computation/1l/11lb/11lb.fit
pddf	/app/data/pr_computation/1l/11lb/11lb.pr.out
profile	/app/data/saxs_computation/1l/11lb/11lb.dat

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

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

Entity 3 non-polymer

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)