SAXSdb — 9rus

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1. Structure Basics

entry_id	9rus
deposition_date	2025-07-04
title	Structure of WRN in complex with ATPgS and Compound 3
keywords	DNA Damage Repair, Inhibitor, Complex, Helicase, HYDROLASE; HYDROLASE
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	32.60 Å
rg_electron	32.34 Å
i0	139637000.00
molecular_weight	92766.0 kDa
excluded_volume	115620 Å³
envelope_volume	150040 Å³
shell_volume	39273 Å³
envelope_diameter	107.9 Å
shell_rg	38.71 Å
envelope_rg	31.96 Å
shape_rg	32.34 Å
total_rg	32.84 Å
total_atoms	6466
n_residues	806
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	109.2 Å
rg_real	32.70 Å
rg_real_error	0.73 Å
i0_real	1.3960e+08
i0_real_error	2.0240e+06
rg_reciprocal	32.66 Å
i0_reciprocal	139600000.0000
total_estimate	0.8797
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.4 Å
skewness	0.396
kurtosis	-0.413
angular_range	— – 0.2450 Å⁻¹
current_alpha	0.0000
highest_alpha	42840000.0000
n_real_points	50
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.892

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	;Bifunctional 3'-5' exonuclease/ATP-dependent helicase WRN ;
formula_weight	48597.1 kDa
ec_number	3.1.-.-,5.6.2.4
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	7456

GMNEGEEDDDKDFLWPAPNEEQVTCLKMYFGHSSFKPVQWKVIHSVLEERRDNVAVMATGYGKSLCFQYPPVYVGKIGLVISPLISLMEDQVLQLKMSNIPACFLGSAQSENVLTDIKLGKYRIVYVTPEYCSGNMGLLQQLEADIGITLIAVDEAHCISEWGHDFRDSFRKLGSLKTALPMVPIVALTATASSSIREDIVRCLNLRNPQITCTGFDRPNLYLEVRRKTGNILQDLQPFLVKTSSHWEFEGPTIIYCPSRKMTQQVTGELRKLNLSCGTYHAGMSFSTRKDIHHRFVRDEIQCVIATIAFGMGINKADIRQVIHYGAPKDMESYYQEIGRAGRDGLQSSCHVLWAPADINLNRHLLTEIRNEKFRLYKLKMMAKMEKYLHSSRCRRQIILSHFEDKQVQKASLGIMGTEKCCDNCRS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
formula_weight	523.2 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	1-[(4-fluorophenyl)methyl]benzimidazole
formula_weight	226.2 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	ADENOSINE-5'-DIPHOSPHATE
formula_weight	427.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	ZINC ION
formula_weight	65.4 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	180

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6. Citations (1)

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length_a	91.173 Å
length_b	91.173 Å
length_c	242.126 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	—

resolution	2.193 Å
resolution_low	85.320 Å
r_factor	0.2686
r_work	0.2670
r_free	0.2978

fit	/app/data/saxs_computation/ru/9rus/9rus.fit
pddf	/app/data/pr_computation/ru/9rus/9rus.pr.out
profile	/app/data/saxs_computation/ru/9rus/9rus.dat

Structure of WRN in complex with ATPgS and Compound 3

SAXS Profile

P(r) Distribution