SAXSdb — 4j7m

▼

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

Protein Dom3Z

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–RNA	Monomer	Protein 1 RNA 1	;RNA (5'-R(PUP(U37)P(U37)PUP*U)-3') ; × 1 ;URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) ; × 2 CALCIUM ION × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DOM3Z_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–378； UniProt 27–384

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4j7m
Deposition date deposition_date	2013-02-13
Structure title title	Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion
Keywords keywords	;Decapping, 5'-3' exoribonuclease, HYDROLASE, HYDROLASE-RNA complex ;; HYDROLASE/RNA
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4j7m__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4j7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4j7m__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	21.64 Å
Rg (electron density)	20.43 Å
Total Rg	21.30 Å
Atom count	3025
Residues	361
Excluded volume	52880 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4j7m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Protein Dom3Z
Molecular weight formula_weight	43132.5 kDa
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	3567

MGSSHHHHHHSSGLVPRGSHPSLRTQPSLYSGPFPFYRRPSELGCFSLDAQRQYHGDARALRYYSPPPINGPGPDFDLRDGYPDRYQPRDEEVQERLDHLLRWVLEHRNQLEGGPGWLAGATVTWRGHLTKLLTTPYERQEGWQLAASRFQGTLYLSEVETPAARAQRLARPPLLRELMYMGYKFEQYMCADKPGGSPDPSGEVNTNVAYCSVLRSRLGNHPLLFSGEVDCLNPQAPCTQPPSCYVELKTSKEMHSPGQWRSFYRHKLLKWWAQSFLPGVPHVVAGFRNPEGFVCSLKTFPTMEMFENVRNDREGWNPSVCMNFCAAFLSFAQSTVVQDDPRLVHLFSWEPGGPVTVSVHRDAPYAFLPSWYVETMTQ

Source Source

Source organism organism	Mus musculus
Common name common_name	mouse
NCBI taxonomy ID ncbi_taxonomy_id	10090
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;RNA (5'-R(PUP(U37)P(U37)PUP*U)-3') ;
Molecular weight formula_weight	1518.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

UUUUU

Entity 3 Entity 3 non-polymer

Description description	;URIDINE 3',5'-BIS(DIHYDROGEN PHOSPHATE) ;
Molecular weight formula_weight	404.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	461

▶

Unit-cell length a length_a	49.985 Å
Unit-cell length b length_b	87.837 Å
Unit-cell length c length_c	54.356 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	111.69 °
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	1.700 Å
Low-resolution limit resolution_low	29.230 Å
R factor r_factor	0.1830
R_work r_work	0.1830
R_free r_free	0.2130

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion

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

Protein Dom3Z

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4j7m__assembly_1__model_1

4j7m__assembly_1__model_1 | I(q)

4j7m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Crystal structure of mouse DXO in complex with substrate mimic RNA and calcium ion

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

Protein Dom3Z

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4j7m__assembly_1__model_1

4j7m__assembly_1__model_1 | I(q)

4j7m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)