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9yhw

;DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:A captured at pre-catalytic stage ;

Method: X-RAY DIFFRACTION D_max: 82.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yhw
deposition_date	2025-10-01
last_revision	2025-12-31
title	;DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:A captured at pre-catalytic stage ;
keywords	DNA binding protein, DNA repair, BER, Human DNA Ligase 1, LIGASE, LIGASE-DNA complex; LIGASE/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	26.68 Å
rg_electron	26.15 Å
i0	119411000.00
molecular_weight	79748.0 kDa
excluded_volume	97089 Å³
envelope_volume	120070 Å³
shell_volume	37065 Å³
envelope_diameter	85.8 Å
shell_rg	34.65 Å
envelope_rg	26.11 Å
shape_rg	26.19 Å
total_rg	26.83 Å
total_atoms	5574
n_residues	676
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	82.7 Å
rg_real	26.51 Å
rg_real_error	0.34 Å
i0_real	1.1940e+08
i0_real_error	1.6370e+06
rg_reciprocal	26.57 Å
i0_reciprocal	119400000.0000
total_estimate	0.9022
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.7 Å
skewness	0.160
kurtosis	-0.460
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	19700000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.914; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.992

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	DNA ligase 1
formula_weight	74213.5 kDa
ec_number	6.5.1.1
mutation	E346A, E592A
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5781

DPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLALGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQADNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGSDPEDTAAALEHHHHHH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	;DNA (5'-D(PGPCPTPGPAPTPGPCPGPTP*(8OG))-3') ;
formula_weight	3421.2 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GCTGATGCGTG

Entity 3 polymer

description	;DNA (5'-D(P(AMP)PGPTPCPGPGPAPC)-3') ;
formula_weight	2467.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

XGTCGGAC

Entity 4 polymer

description	;DNA (5'-D(PGPTPCPCPGPAPCPAPAPCPGPCPAPTPCPAPGPC)-3') ;
formula_weight	5470.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GTCCGACAACGCATCAGC

Entity 5 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	5

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	195

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6. Citations (1)

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length_a	74.490 Å
length_b	100.122 Å
length_c	115.239 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.560 Å
resolution_low	29.860 Å
r_factor	0.1855
r_work	0.1822
r_free	0.2293

fit	/app/data/saxs_computation/yh/9yhw/9yhw.fit
pddf	/app/data/pr_computation/yh/9yhw/9yhw.pr.out
profile	/app/data/saxs_computation/yh/9yhw/9yhw.dat

;DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxodG:A captured at pre-catalytic stage ;

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 (6)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)