SAXSdb — 3bca

▼

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

O-phosphoseryl-tRNA(Sec) selenium transferase

Mus musculus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 4	IODIDE ION × 248 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	SPCS_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–450； UniProt 19–468

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	3bca
Deposition date deposition_date	2007-11-12
Structure title title	Crystal structure of mouse selenocysteine synthase, sodium iodide soak
Keywords keywords	;disorder-order transition, phosphate-loop, pyridoxal phosphate, selenocysteine synthase (SecS, SepSecS), soluble liver antigen/liver and pancreas antigen (SLA/LP), Protein biosynthesis, Selenium, Transferase ;; TRANSFERASE
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.

3bca__assembly_1__model_1

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

Download this curve (.dat)

3bca__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bca__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	39.23 Å
Rg (electron density)	38.45 Å
Total Rg	39.00 Å
Atom count	13828
Residues	1740
Excluded volume	251220 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bca__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	O-phosphoseryl-tRNA(Sec) selenium transferase
Molecular weight formula_weight	49979.8 kDa
EC 编号 ec_number	2.9.1.-
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	3778

RQGCEARRAHEHLIRLLLEQGKCPEDGWDESTLELFLHELAVMDSNNFLGNCGVGEREGRVASALVARRHYRFIHGIGRSGDISAVQPKAAGSSLLNKITNSLVLNVIKLAGVHSVASCFVVPMATGMSLTLCFLTLRHKRPKAKYIIWPRIDQKSCFKSMVTAGFEPVVIENVLEGDELRTDLKAVEAKIQELGPEHILCLHSTTACFAPRVPDRLEELAVICANYDIPHVVNNAYGLQSSKCMHLIQQGARVGRIDAFVQSLDKNFMVPVGGAIIAGFNEPFIQDISKMYPGRASASPSLDVLITLLSLGCSGYRKLLKERKEMFVYLSTQLKKLAEAHNERLLQTPHNPISLAMTLKTIDGHHDKAVTQLGSMLFTRQVSGARAVPLGNVQTVSGHTFRGFMSHADNYPCAYLNAAAAIGMKMQDVDLFIKRLDKCLNIVRKEQTRA

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	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	62

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	264

▼

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3bcaa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.9 — SepSecS-like

CATH v4.4 (3 domains)

Domain ID domain_id	3bcaA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	2160 —

Domain ID domain_id	3bcaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	3bcaA03
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1150 — Aspartate Aminotransferase, domain 1
Homologous superfamily homologous superfamily	10 — Aspartate Aminotransferase, domain 1

▶

Unit-cell length a length_a	59.222 Å
Unit-cell length b length_b	138.371 Å
Unit-cell length c length_c	141.520 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1853
R_work r_work	0.1826
R_free r_free	0.2357

Crystal structure of mouse selenocysteine synthase, sodium iodide soak

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

O-phosphoseryl-tRNA(Sec) selenium transferase

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

3bca__assembly_1__model_1

3bca__assembly_1__model_1 | I(q)

3bca__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) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal structure of mouse selenocysteine synthase, sodium iodide soak

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

O-phosphoseryl-tRNA(Sec) selenium transferase

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

3bca__assembly_1__model_1

3bca__assembly_1__model_1 | I(q)

3bca__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) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

7. Citations (1)