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9yhu

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

Method: X-RAY DIFFRACTION D_max: 82.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yhu
deposition_date	2025-10-01
last_revision	2025-12-31
title	;DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:A captured at post-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	26.70 Å
rg_electron	26.17 Å
i0	117272000.00
molecular_weight	78954.0 kDa
excluded_volume	96173 Å³
envelope_volume	119280 Å³
shell_volume	36835 Å³
envelope_diameter	86.9 Å
shell_rg	34.47 Å
envelope_rg	26.11 Å
shape_rg	26.20 Å
total_rg	26.89 Å
total_atoms	5524
n_residues	667
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	82.0 Å
rg_real	26.53 Å
rg_real_error	0.38 Å
i0_real	1.1730e+08
i0_real_error	1.6280e+06
rg_reciprocal	26.59 Å
i0_reciprocal	117300000.0000
total_estimate	0.9047
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.161
kurtosis	-0.457
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	19370000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.925; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.991

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

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	5973

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(8GM)PGPTPCPGPGPAPC)-3') ;
formula_weight	5620.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	B

GCTGATGCGTXGTCGGAC

Entity 3 polymer

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

Polymer

type	polydeoxyribonucleotide
strand_id	C

GTCCGACAACGCATCAGC

Entity 4 non-polymer

description	ADENOSINE MONOPHOSPHATE
formula_weight	347.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	428

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6. Citations (1)

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length_a	74.668 Å
length_b	101.941 Å
length_c	116.004 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	1.960 Å
resolution_low	24.560 Å
r_factor	0.1725
r_work	0.1715
r_free	0.2035

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

;DNA ligase 1 E346A/E592A in complex with nick containing 3'-8oxorG:A captured at post-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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)