SAXSdb — 10yz

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Decapping and exoribonuclease protein

Mus musculus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 1–397	Not recorded	;RNA (5'-R(GPGPGPUPU)-3') ; × 1 MAGNESIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.60 Å R-free 0.211

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 10YZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
11AO Crystal structure of mouse DXO in complex with the oligonucleotide pA5 with 5'phosphate in the product and substrate states Deposited 2026-02-13	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–384（358 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.59 Å R-free 0.190
11AP Crystal structure of mouse DXO in complex with the UDP-N-acetylglucosamine cap Deposited 2026-02-13	Different construct Different oligomeric state Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–384（358 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å R-free 0.206
3FQI Crystal Structure of the Mouse Dom3Z Deposited 2009-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–397（397 aa）	Not recorded	MG MAGNESIUM ION × 1 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.1 M Hepes (pH 7.5) and 20% (w/v) PEG 8000, vapor diffusion, sitting drop, temperature 295K	Resolution 2.01 Å R-free 0.283
3FQJ Crystal Structure of the Mouse Dom3Z in Complex with GDP Deposited 2009-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–397（397 aa）	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；0.2 M potassium phosphate monobasic and 25% (w/v) PEG 3350, pH 7.5, vapor diffusion, sitting drop, temperature 295K	Resolution 2.62 Å R-free 0.267
4J7L Crystal structure of mouse DXO in complex with PRODUCT RNA AND two MAGNESIUM ions Deposited 2013-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 27–384（358 aa）	Not recorded	UBD URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% w/v PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.80 Å R-free 0.215
4J7M Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion Deposited 2013-02-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 27–384（358 aa）	Not recorded	UBD URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.213
4J7N Crystal structure of mouse DXO in complex with M7GPPPG cap Deposited 2013-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–384（358 aa）	Not recorded	GTG 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE × 2 9MG 9-METHYLGUANINE × 1 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% w/v PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.50 Å R-free 0.200
5ULI Crystal Structure of mouse DXO in complex with (3'-NADP)+ and calcium ion Deposited 2017-01-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–384（358 aa）	Not recorded	CA CALCIUM ION × 1 0WD [[(2R,3S,4R,5R)-5-(3-aminocarbonyl-4H-pyridin-1-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methyl hydrogen phosphate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% (w/v) PEG 3350	Resolution 2.10 Å R-free 0.208
6AIX Crystal structure of DXO in complex with adenosine 3', 5' bisphosphate and two magnesium ions Deposited 2018-08-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–384（358 aa）	Not recorded	A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 100mM pAp, 10mM MgCl2	Resolution 1.80 Å R-free 0.199
6AIY Crystal structure of DXO (E234A mutant) in complex with adenosine 3', 5' bisphosphate and two magnesium ions Deposited 2018-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 27–384（358 aa）	Mutation：E234A	A3P ADENOSINE-3'-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20% (w/v) PEG 3350, 100mM pAp, 10mM MgCl2	Resolution 1.90 Å R-free 0.203
6WRE Crystal structure of mouse DXO in complex with 5'-OH RNA substrate mimic and calcium ion Deposited 2020-04-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 27–384（358 aa）	Not recorded	CA CALCIUM ION × 1 U3P 3'-URIDINEMONOPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% (w/v) PEG 3350	Resolution 2.00 Å R-free 0.220
6WUF Crystal structure of mouse DXO in complex with 3'-FADP Deposited 2020-05-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–397（397 aa）	Mutation：E192S/E234Q/E253Q	UBG [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(7,8-dimethyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；23% (w/v) PEG3350	Resolution 1.60 Å R-free 0.234
6WUK Crystal structure of mouse DXO in complex with CoA Deposited 2020-05-04	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–397（397 aa）	Mutation：E192S/E234Q/E253Q	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；23% (w/v) PEG3350	Resolution 1.60 Å R-free 0.214

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DXO_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–397； UniProt 1–397

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	10yz
Deposition date deposition_date	2026-02-12
最后修订 last_revision	2026-06-10
Structure title title	Crystal structure of mouse DXO in complex with pGGGUU RNA and two magnesium ions
Keywords keywords	dxo, RNA, decapping, exoribonuclease, HYDROLASE, HYDROLASE-RNA complex; HYDROLASE/RNA
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	21.39 Å
Radius of gyration Rg (electron density) rg_electron	20.30 Å
Forward intensity I(0) i0	32307700.00
Molecular weight molecular_weight	42082.0 kDa
Excluded volume excluded_volume	51900 Å³
Envelope volume envelope_volume	61495 Å³
Hydration-shell volume shell_volume	24689 Å³
Envelope diameter envelope_diameter	68.4 Å
Shell Rg shell_rg	27.45 Å
Envelope Rg envelope_rg	20.39 Å
Shape Rg shape_rg	20.31 Å
Total Rg total_rg	21.17 Å
Total atoms total_atoms	2964
Residues n_residues	362
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.8 Å
Rg (real space) rg_real	21.23 Å
Rg uncertainty (real space) rg_real_error	0.28 Å
I(0) (real space) i0_real	3.2310e+07
I(0) uncertainty (real space) i0_real_error	3.4560e+05
Rg (reciprocal space) rg_reciprocal	21.26 Å
I(0) (reciprocal space) i0_reciprocal	32310000.0000
Solution quality estimate total_estimate	0.6516
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.5 Å
Skewness Skewness skewness	0.150
Kurtosis Kurtosis kurtosis	-0.397
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10850000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria 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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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Decapping and exoribonuclease protein
Molecular weight formula_weight	45336.3 kDa
EC 编号 ec_number	3.6.1.-,3.1.13.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3331

MEPRGTKRKAEKTEVEKPLNKLPRAVPSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFEQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGEVDCLNPQAPCTQPPSCYVELKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQDLPPLSKTPSPKD

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(GPGPGPUPU)-3') ;
Molecular weight formula_weight	1603.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

GGGUU

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	323

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8. Citations (1)

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Unit-cell length a length_a	46.365 Å
Unit-cell length b length_b	87.999 Å
Unit-cell length c length_c	50.156 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.37 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	42.230 Å
R factor r_factor	0.1845
R_work r_work	0.1834
R_free 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

1. Protein Identity and Related Structures Protein Identity & Related Structures

Decapping and exoribonuclease protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)