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11ao

;Crystal structure of mouse DXO in complex with the oligonucleotide pA5 with 5'phosphate in the product and substrate states ;

Method: X-RAY DIFFRACTION D_max: 68.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	11ao
deposition_date	2026-02-13
last_revision	2026-06-10
title	;Crystal structure of mouse DXO in complex with the oligonucleotide pA5 with 5'phosphate in the product and substrate states ;
keywords	DXO/Rai1 enzyme, pA5 RNA, RNA BINDING PROTEIN, Protein Dom3Z; 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	21.39 Å
rg_electron	20.32 Å
i0	31947800.00
molecular_weight	42051.0 kDa
excluded_volume	51886 Å³
envelope_volume	61513 Å³
shell_volume	24680 Å³
envelope_diameter	68.4 Å
shell_rg	27.47 Å
envelope_rg	20.41 Å
shape_rg	20.33 Å
total_rg	21.16 Å
total_atoms	2962
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	68.0 Å
rg_real	21.24 Å
rg_real_error	0.29 Å
i0_real	3.1950e+07
i0_real_error	3.5730e+05
rg_reciprocal	21.27 Å
i0_reciprocal	31950000.0000
total_estimate	0.8876
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	28.0 Å
skewness	0.147
kurtosis	-0.399
angular_range	— – 0.3700 Å⁻¹
current_alpha	0.0000
highest_alpha	9748000.0000
n_real_points	69
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.857; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.973

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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	3298

PSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFEQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGEVDCLNPQAPCTQPPSCYVELKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQ

Source

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

Entity 2 polymer

description	;RNA (5'-R(APAPAPA)-3') ;
formula_weight	1271.9 kDa
src_method	syn
entity_count	1

Polymer

type	polyribonucleotide
strand_id	B

AAAA

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	289

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6. Citations (1)

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length_a	49.996 Å
length_b	88.253 Å
length_c	53.142 Å
angle_alpha	90.00 °
angle_beta	113.18 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.590 Å
resolution_low	48.850 Å
r_factor	0.1816
r_work	0.1812
r_free	0.1895

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

;Crystal structure of mouse DXO in complex with the oligonucleotide pA5 with 5'phosphate in the product and substrate states ;

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)