SAXSdb — 6wuk

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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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–397	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

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 6WUK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10YZ Crystal structure of mouse DXO in complex with pGGGUU RNA and two magnesium ions Deposited 2026-02-12	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–397（397 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å R-free 0.211
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 mutation/modification 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	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 mutation/modification 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	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 mutation/modification 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 mutation/modification 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 mutation/modification Different oligomeric state 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 ligand/ion 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

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 21–417； 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	6wuk
Deposition date deposition_date	2020-05-04
Structure title title	Crystal structure of mouse DXO in complex with CoA
Keywords keywords	DXO, decapping, CoA, Coenzyme A, cap, HYDROLASE; HYDROLASE
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	21.37 Å
Radius of gyration Rg (electron density) rg_electron	20.25 Å
Forward intensity I(0) i0	30868000.00
Molecular weight molecular_weight	41624.0 kDa
Excluded volume excluded_volume	51553 Å³
Envelope volume envelope_volume	60679 Å³
Hydration-shell volume shell_volume	24376 Å³
Envelope diameter envelope_diameter	69.6 Å
Shell Rg shell_rg	27.36 Å
Envelope Rg envelope_rg	20.41 Å
Shape Rg shape_rg	20.26 Å
Total Rg total_rg	21.08 Å
Total atoms total_atoms	2933
Residues n_residues	358
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	68.3 Å
Rg (real space) rg_real	21.22 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	3.0870e+07
I(0) uncertainty (real space) i0_real_error	3.8740e+05
Rg (reciprocal space) rg_reciprocal	21.25 Å
I(0) (reciprocal space) i0_reciprocal	30870000.0000
Solution quality estimate total_estimate	0.6930
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.1 Å
Skewness Skewness skewness	0.157
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7058000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.854; Stabil: 1.000; Sysdev: 0.161; Positv: 1.000; Valcen: 0.992; Smooth: 0.967

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Decapping and exoribonuclease protein
Molecular weight formula_weight	47463.6 kDa
EC 编号 ec_number	3.1.13.-,3.6.1.-
Mutation mutation	E192S/E234Q/E253Q
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	3348

MGSSHHHHHHSSGLVPRGSHMEPRGTKRKAEKTEVEKPLNKLPRAVPSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFSQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGQVDCLNPQAPCTQPPSCYVQLKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQDLPPLSKTPSPKD

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	380

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8. Citations (1)

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Unit-cell length a length_a	49.862 Å
Unit-cell length b length_b	87.665 Å
Unit-cell length c length_c	54.023 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	112.24 °
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	1.599 Å
Low-resolution limit resolution_low	50.005 Å
R factor r_factor	0.1856
R_work r_work	0.1846
R_free r_free	0.2143

fit	/app/data/saxs_computation/wu/6wuk/6wuk.fit
pddf	/app/data/pr_computation/wu/6wuk/6wuk.pr.out
profile	/app/data/saxs_computation/wu/6wuk/6wuk.dat

Crystal structure of mouse DXO in complex with CoA

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