SAXSdb — 1vlr

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

mRNA decapping enzyme

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	1,2-ETHANEDIOL × 6 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DCPS_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–350； UniProt 1–338 Author chain B； PDBConstruct 13–350； UniProt 1–338

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	1vlr
Deposition date deposition_date	2004-08-10
Structure title title	Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution
Keywords keywords	;16740816, mRNA decapping enzyme (DcpS), STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, Joint Center for Structural Genomics, RNA BINDING PROTEIN ;; RNA BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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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.

1vlr__assembly_1__model_1

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

Download this curve (.dat)

1vlr__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1vlr__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.20 Å
Rg (electron density)	26.00 Å
Total Rg	26.88 Å
Atom count	4802
Residues	582
Excluded volume	85780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1vlr__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	mRNA decapping enzyme
Molecular weight formula_weight	40504.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5721

MGSDKIHHHHHHMADTAPQLKRKREQEAEEAETPSTEEKEAGVGNGTSAPVRLPFSGFRVQKVLRESARDKIIFLHGKVNEDSGDTHGEDAVVILEKTPFQVEHVAQLLTGSPELKLQFSNDIYSTYNLFPPRHLSDIKTTVVYPATEKHLQKYMRQDLRLIRETGDDYRTITLPYLESQSLSIQWVYNILDKKAEADRIVFENPDPSDGFVLIPDLKWNQQQLDDLYLIAICHRRGIRSLRDLTPEHLPLLRNILREGQEAILKRYQVTGDRLRVYLHYLPSYYHLHVHFTALGFEAPGSGVERAHLLAQVIENLECDPKHYQQRTLTFALRTDDPLLQLLQKAQQERN

Source Source

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

Entity 2 Entity 2 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	806

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6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1vlra1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d1vlra2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.1 — mRNA decapping enzyme DcpS N-terminal domain

Domain ID domain_id	d1vlrb1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.13 — HIT-like
Superfamily Superfamily superfamily	d.13.1 — HIT-like
Family Family family	d.13.1.3 — mRNA decapping enzyme DcpS C-terminal domain

Domain ID domain_id	d1vlrb2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.246 — mRNA decapping enzyme DcpS N-terminal domain
Superfamily Superfamily superfamily	d.246.1 — mRNA decapping enzyme DcpS N-terminal domain
Family Family family	d.246.1.1 — mRNA decapping enzyme DcpS N-terminal domain

CATH v4.4 (6 domains)

Domain ID domain_id	1vlrA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	1vlrA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2240 — mRNA decapping enzyme DcpS N-terminal fold
Homologous superfamily homologous superfamily	10 — mRNA decapping enzyme DcpS N-terminal domain

Domain ID domain_id	1vlrA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

Domain ID domain_id	1vlrB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	40 — Scavenger mRNA decapping enzyme, N-terminal domain

Domain ID domain_id	1vlrB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	2240 — mRNA decapping enzyme DcpS N-terminal fold
Homologous superfamily homologous superfamily	10 — mRNA decapping enzyme DcpS N-terminal domain

Domain ID domain_id	1vlrB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	428 — HIT family, subunit A
Homologous superfamily homologous superfamily	10 — HIT-like

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Unit-cell length a length_a	65.399 Å
Unit-cell length b length_b	59.231 Å
Unit-cell length c length_c	100.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.80 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.830 Å
Low-resolution limit resolution_low	37.580 Å
R factor r_factor	0.1605
R_work r_work	0.1584
R_free r_free	0.2010

Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution

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

mRNA decapping enzyme

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

1vlr__assembly_1__model_1

1vlr__assembly_1__model_1 | I(q)

1vlr__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of mRNA decapping enzyme (DcpS) from Mus musculus at 1.83 A resolution

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

mRNA decapping enzyme

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

1vlr__assembly_1__model_1

1vlr__assembly_1__model_1 | I(q)

1vlr__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

7. Citations (1)