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9wjk

Crystal structure of mouse EOGT-UDP complex

Method: X-RAY DIFFRACTION D_max: 81.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9wjk
deposition_date	2025-08-31
last_revision	2026-05-27
title	Crystal structure of mouse EOGT-UDP complex
keywords	O-GlcNAc, Glycosyltransferase, ER protein, TRANSFERASE; TRANSFERASE
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	25.09 Å
rg_electron	24.13 Å
i0	54224400.00
molecular_weight	57158.0 kDa
excluded_volume	71374 Å³
envelope_volume	83446 Å³
shell_volume	28738 Å³
envelope_diameter	84.2 Å
shell_rg	31.56 Å
envelope_rg	24.47 Å
shape_rg	24.10 Å
total_rg	25.07 Å
total_atoms	4034
n_residues	480
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	81.5 Å
rg_real	25.05 Å
rg_real_error	0.56 Å
i0_real	5.4220e+07
i0_real_error	8.4250e+05
rg_reciprocal	25.06 Å
i0_reciprocal	54220000.0000
total_estimate	0.8931
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.324
kurtosis	-0.274
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	6908000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.990

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	EGF domain-specific O-linked N-acetylglucosamine transferase
formula_weight	58278.9 kDa
ec_number	2.4.1.255
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	4326

GPALYDYSSLRLPAEHIPFFLHNNRHVASVCREDSHCPYKKHLENLNYCWGYEKSCAPEFRFGSPVCSYVDLGWTDTLESAQDMFWRQADFGYARERLGEIRTICQPERASDSSLVCSRYLQYCRATGLYLDLRNIKRNHDRFKEDFLQGGEIGGYCKLDSHALVSEGQRKSPLQSWFAELQGYTQLNFRPIEDAKCDIVVEKPTYFMKLDAGINMYHHFCDFLNLYLTQHVNNSFSTDVYIVMWDTSTYGYGDLFSDTWKAFTDYDVIHLKTYDSKKVCFKEAVFSLLPRMRYGLFYNTPLISGCQNTGLFRAFSQHVLHRLNITQEGPKDGKVRVTILARSTEYRKILNQDELVNALKTVSTFEVRVVDYKYRELGFLDQLRITHNTDIFIGMHGAGLTHLLFLPDWAAVFELYNCEDERCYLDLARLRGIHYITWRKPSKVFPQDKGHHPTLGEHPKFTNYSFDVEEFMYLVLQAAEHVLQHPQWPFKKKHDEL

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Homo sapiens

Entity 2 branched

description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	424.4 kDa
src_method	man
entity_count	1

Entity 3 non-polymer

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

Entity 4 non-polymer

description	URIDINE-5'-DIPHOSPHATE
formula_weight	404.2 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	292

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6. Citations (1)

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length_a	54.914 Å
length_b	58.635 Å
length_c	179.354 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 2 21
int_tables_number	18
crystal_system	orthorhombic

resolution	1.800 Å
resolution_low	49.080 Å
r_factor	0.1708
r_work	0.1693
r_free	0.2002

fit	/app/data/saxs_computation/wj/9wjk/9wjk.fit
pddf	/app/data/pr_computation/wj/9wjk/9wjk.pr.out
profile	/app/data/saxs_computation/wj/9wjk/9wjk.dat