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11ap

Crystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap

Method: X-RAY DIFFRACTION D_max: 67.4 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ap
deposition_date	2026-02-13
last_revision	2026-06-10
title	Crystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap
keywords	;Noncanonical RNA cap, DXO/Rai1 family of enzymes UDP-glucose (UDP-Glc) and UDP-N-acetylglucosamine (UDP-GlcNAc), RNA BINDING PROTEIN, DXO ;; RNA BINDING PROTEIN
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	21.41 Å
rg_electron	20.29 Å
i0	30779000.00
molecular_weight	41632.0 kDa
excluded_volume	51542 Å³
envelope_volume	60713 Å³
shell_volume	24368 Å³
envelope_diameter	68.8 Å
shell_rg	27.44 Å
envelope_rg	20.41 Å
shape_rg	20.31 Å
total_rg	21.11 Å
total_atoms	2930
n_residues	358
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	67.4 Å
rg_real	21.26 Å
rg_real_error	0.33 Å
i0_real	3.0780e+07
i0_real_error	3.6800e+05
rg_reciprocal	21.29 Å
i0_reciprocal	30780000.0000
total_estimate	0.8927
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	27.8 Å
skewness	0.154
kurtosis	-0.401
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	6980000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.978

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Decapping and exoribonuclease protein
formula_weight	40961.2 kDa
ec_number	3.6.1.-,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3365

PSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFEQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGEVDCLNPQAPCTQPPSCYVELKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQ

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli BL21(DE3)

Entity 2 non-polymer

description	URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
formula_weight	607.4 kDa
src_method	syn
entity_count	1

Entity 3 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	423

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6. Citations (1)

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length_a	49.880 Å
length_b	87.990 Å
length_c	53.580 Å
angle_alpha	90.00 °
angle_beta	113.03 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.800 Å
resolution_low	49.310 Å
r_factor	0.1670
r_work	0.1648
r_free	0.2064

fit	/app/data/saxs_computation/1a/11ap/11ap.fit
pddf	/app/data/pr_computation/1a/11ap/11ap.pr.out
profile	/app/data/saxs_computation/1a/11ap/11ap.dat

Crystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap

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