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11fc

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

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	11fc
deposition_date	2026-02-20
last_revision	2026-04-29
title	E.Coli DNA Topoisomerase 3 in complex with an 8mer ssDNA oligo CTGAACTT
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	30.16 Å
rg_electron	29.84 Å
i0	89722600.00
molecular_weight	72821.0 kDa
excluded_volume	90522 Å³
envelope_volume	118860 Å³
shell_volume	34370 Å³
envelope_diameter	103.1 Å
shell_rg	35.73 Å
envelope_rg	29.71 Å
shape_rg	29.85 Å
total_rg	30.33 Å
total_atoms	5117
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	102.5 Å
rg_real	30.23 Å
rg_real_error	0.82 Å
i0_real	8.9720e+07
i0_real_error	1.3640e+06
rg_reciprocal	30.20 Å
i0_reciprocal	89720000.0000
total_estimate	0.8775
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.9 Å
skewness	0.413
kurtosis	-0.284
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	16300000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.846; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.956; Smooth: 0.910

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	5257

MRLFIAEKPSLARAIADVLPKPHRKGDGFIECGNGQVVTWCIGHLLEQAQPDAYDSRYARWNLADLPIVPEKWQLQPRPSVTKQLNVIKRFLHEASEIVHAGDPDREGQLLVDEVLDYLQLAPEKRQQVQRCLINDLNPQAVERAIDRLRSNSEFVPLCVSALARARADWLYGINMTRAYTILGRNAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVAKDFFEVKAHIVTPADERFTAIWQPSEACEPYQDEEGRLLHRPLAEHVVNRISGQPAIVTSYNDKRESESAPLPFSLSALQIEAAKRFGLSAQNVLDICQKLYETHKLITYPRSDCRYLPEEHFAGRHAVMNAISVHAPDLLPQPVVDPDIRNRCWDDKKVDAHHAIIPTARSSAINLTENEAKVYNLIARQYLMQFCPDAVFRKCVIELDIAKGKFVAKARFLAEAGWRTLLGSKERDEENDGTPLPVVAKGDELLCEKGEVVERQTQPPRHFTDATLLSAMTGIARFVQDKDLKKILRATDGLGTEATRAGIIELLFKRGFLTKKGRYIHSTDAGKALFHSLPEMATRPDMTAHWESVLTQISEKQCRYQDFMQPLVGTLYQLIDQAKRTPVRQFRGIVAPGSGGSADKKKAAPRKRSAKKENLYFQ

Source

organism	Escherichia coli
ncbi_taxonomy_id	562
host_organism	Escherichia coli

Entity 2 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	B

CTGAACTT

Entity 3 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	6

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	135

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6. Citations (1)

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length_a	109.794 Å
length_b	133.242 Å
length_c	78.434 Å
angle_alpha	90.00 °
angle_beta	133.98 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.100 Å
resolution_low	34.310 Å
r_factor	0.2291
r_work	0.2272
r_free	0.2646

fit	/app/data/saxs_computation/1f/11fc/11fc.fit
pddf	/app/data/pr_computation/1f/11fc/11fc.pr.out
profile	/app/data/saxs_computation/1f/11fc/11fc.dat

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

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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)