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10yz

Crystal structure of mouse DXO in complex with pGGGUU RNA and two magnesium ions

Method: X-RAY DIFFRACTION D_max: 66.8 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	10yz
deposition_date	2026-02-12
last_revision	2026-06-10
title	Crystal structure of mouse DXO in complex with pGGGUU RNA and two magnesium ions
keywords	dxo, RNA, decapping, exoribonuclease, HYDROLASE, HYDROLASE-RNA complex; HYDROLASE/RNA
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	21.39 Å
rg_electron	20.30 Å
i0	32307700.00
molecular_weight	42082.0 kDa
excluded_volume	51900 Å³
envelope_volume	61495 Å³
shell_volume	24689 Å³
envelope_diameter	68.4 Å
shell_rg	27.45 Å
envelope_rg	20.39 Å
shape_rg	20.31 Å
total_rg	21.17 Å
total_atoms	2964
n_residues	362
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	66.8 Å
rg_real	21.23 Å
rg_real_error	0.28 Å
i0_real	3.2310e+07
i0_real_error	3.4560e+05
rg_reciprocal	21.26 Å
i0_reciprocal	32310000.0000
total_estimate	0.6516
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	28.5 Å
skewness	0.150
kurtosis	-0.397
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	10850000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 0.281; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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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	45336.3 kDa
ec_number	3.6.1.-,3.1.13.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	3331

MEPRGTKRKAEKTEVEKPLNKLPRAVPSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFEQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGEVDCLNPQAPCTQPPSCYVELKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQDLPPLSKTPSPKD

Source

organism	Mus musculus
common_name	house mouse
ncbi_taxonomy_id	10090
host_organism	Escherichia coli

Entity 2 polymer

description	;RNA (5'-R(GPGPGPUPU)-3') ;
formula_weight	1603.0 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	C

GGGUU

Entity 3 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	323

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6. Citations (1)

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length_a	46.365 Å
length_b	87.999 Å
length_c	50.156 Å
angle_alpha	90.00 °
angle_beta	114.37 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.600 Å
resolution_low	42.230 Å
r_factor	0.1845
r_work	0.1834
r_free	0.2110

fit	/app/data/saxs_computation/0y/10yz/10yz.fit
pddf	/app/data/pr_computation/0y/10yz/10yz.pr.out
profile	/app/data/saxs_computation/0y/10yz/10yz.dat

Crystal structure of mouse DXO in complex with pGGGUU RNA and two magnesium ions

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 (4)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)