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9zd6

Bacterial interstrand DNA crosslink glycosylase AlkX/YcaQ bound to DNA

Method: X-RAY DIFFRACTION D_max: 95.0 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9zd6
deposition_date	2025-11-24
last_revision	2026-01-14
title	Bacterial interstrand DNA crosslink glycosylase AlkX/YcaQ bound to DNA
keywords	DNA glycosylase, interstrand DNA crosslink, hydrolase, HYDROLASE-DNA complex; HYDROLASE/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	30.92 Å
rg_electron	30.54 Å
i0	180968000.00
molecular_weight	97665.0 kDa
excluded_volume	118330 Å³
envelope_volume	156320 Å³
shell_volume	42206 Å³
envelope_diameter	98.7 Å
shell_rg	38.39 Å
envelope_rg	29.75 Å
shape_rg	30.56 Å
total_rg	31.16 Å
total_atoms	6837
n_residues	794
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	95.0 Å
rg_real	30.77 Å
rg_real_error	0.66 Å
i0_real	1.8100e+08
i0_real_error	2.9970e+06
rg_reciprocal	30.83 Å
i0_reciprocal	181000000.0000
total_estimate	0.9087
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	1
r_peak_primary	37.2 Å
skewness	0.173
kurtosis	-0.542
angular_range	— – 0.2550 Å⁻¹
current_alpha	0.0000
highest_alpha	26980000.0000
n_real_points	52
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.966

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Cytoplasmic protein
formula_weight	45664.3 kDa
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	6892

MYESAALPSPRRDATLSLTQARHVALAAQGFADPRPSGTVTAHHLRQVVDRIGVIQIDSVNVLCRSHYLPVYARLGPYDRALLDRAATTPGHFLVEYWAHEASLIPLHTHRLLRWRMADITGAWRIVQRAGEEHPELVRAVLDEVARTGPVTARQVADALRHDLPHSAKRWGWNWSVVKSALEYLFWRGEITANGRNQHFERRYDLTSRVLPAEVHTAPDPDPDDARRQLVAIAARAHGVATERCLRDYFRLSAAHGRAAVRDLVDSGELIPVRVEGWRQPAYLHRDARFPNSVAARALLSPFDSLVWERARIKALFDFHYRLEIYVPAAKRVHGYYVLPFLLGDRLVARVDLKADRASGRLLVRRTTLEDHAPADTMAELSAELDQMAEWLGLPEGVVHSA

Source

organism	Thermobifida fusca
ncbi_taxonomy_id	2021
host_organism	Escherichia coli

Entity 2 polymer

description	;DNA (5'-D(TPGPAPGPTPCPGPT(3DR)PGPAPTPGPAPCPCPAPC)-3') ;
formula_weight	5407.5 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	C

TGAGTCGTNGATGACCAC

Entity 3 polymer

description	;DNA (5'-D(GPTPGPGPTPCPAPTPCPCPAPCPGPAPCPTPCPA)-3') ;
formula_weight	5476.6 kDa
src_method	syn
entity_count	1

Polymer

type	polydeoxyribonucleotide
strand_id	D

GTGGTCATCCACGACTCA

Entity 4 non-polymer

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

Entity 5 non-polymer

description	IODIDE ION
formula_weight	126.9 kDa
src_method	syn
entity_count	1

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	55

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6. Citations (1)

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length_a	56.598 Å
length_b	115.641 Å
length_c	160.676 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.600 Å
resolution_low	50.840 Å
r_factor	0.2094
r_work	0.2068
r_free	0.2555

fit	/app/data/saxs_computation/zd/9zd6/9zd6.fit
pddf	/app/data/pr_computation/zd/9zd6/9zd6.pr.out
profile	/app/data/saxs_computation/zd/9zd6/9zd6.dat

Bacterial interstrand DNA crosslink glycosylase AlkX/YcaQ bound to DNA

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 non-polymer

Entity 5 non-polymer

Entity 6 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)