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9yhy

;DNA ligase 1 wild-type in complex with nick containing 3'-8oxodG:C captured at pre-catalytic stage ;

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9yhy
deposition_date	2025-10-01
last_revision	2025-12-31
title	;DNA ligase 1 wild-type in complex with nick containing 3'-8oxodG:C 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	26.51 Å
rg_electron	25.96 Å
i0	106251000.00
molecular_weight	71097.0 kDa
excluded_volume	84601 Å³
envelope_volume	112430 Å³
shell_volume	35298 Å³
envelope_diameter	86.0 Å
shell_rg	34.11 Å
envelope_rg	25.78 Å
shape_rg	26.01 Å
total_rg	26.63 Å
total_atoms	4985
n_residues	656
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	84.4 Å
rg_real	26.34 Å
rg_real_error	0.60 Å
i0_real	1.0630e+08
i0_real_error	1.6320e+06
rg_reciprocal	26.39 Å
i0_reciprocal	106300000.0000
total_estimate	0.6548
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	33.8 Å
skewness	0.151
kurtosis	-0.466
angular_range	— – 0.3000 Å⁻¹
current_alpha	0.0000
highest_alpha	17600000.0000
n_real_points	61
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 0.291; Positv: 1.000; Valcen: 0.993; Smooth: 0.000

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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	74329.6 kDa
ec_number	6.5.1.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	5015

DPSGYNPAKNNYHPVEDACWKPGQKVPYLAVARTFEKIEEVSARLRMVETLSNLLRSVVALSPPDLLPVLYLSLNHLGPPQQGLELGVGDGVLLKAVAQATGRQLESVRAEAAEKGDVGLVAENSRSTQRLMLPPPPLTASGVFSKFRDIARLTGSASTAKKIDIIKGLFVACRHSEARFIARSLSGRLRLGLAEQSVLAALSQAVSLTPPGQEFPPAMVDAGKGKTAEARKTWLEEQGMILKQTFCEVPDLDRIIPVLLEHGLERLPEHCKLSPGIPLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQEDNTGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQVCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQSVKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLDGVGDTLDLVVIGAYLGRGKRAGRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVLPSPRPYVRIDGAVIPDHWLDPSAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVACLYRKQSQIQNQQGEDSGSDPEDTAAALEHHHHHH

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(PGPTPCPCPGPAPCPCPAPCPGPCPAPTPCPAPGPC)-3') ;
formula_weight	5446.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GTCCGACCACGCATCAGC

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	30

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6. Citations (1)

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length_a	63.511 Å
length_b	115.591 Å
length_c	126.225 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	2.760 Å
resolution_low	24.760 Å
r_factor	0.2324
r_work	0.2280
r_free	0.2828

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

;DNA ligase 1 wild-type in complex with nick containing 3'-8oxodG:C 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 (5)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 polymer

Polymer

Entity 5 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)