SAXSdb — 2d4g

▼

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

hypothetical protein BSU11850

Bacillus subtilis

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	O31629_BACSU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–171； UniProt 1–171 Author chain B； PDBConstruct 1–171； UniProt 1–171

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	2d4g
Deposition date deposition_date	2005-10-19
Structure title title	Structure of YjcG protein, a putative 2'-5' RNA ligase from Bacillus subtilis
Keywords keywords	beta barrel, alpha helix, STRUCTURAL GENOMICS, UNKNOWN FUNCTION; STRUCTURAL GENOMICS, UNKNOWN FUNCTION
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.

2d4g__assembly_1__model_1

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

Download this curve (.dat)

2d4g__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2d4g__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	22.23 Å
Rg (electron density)	20.94 Å
Total Rg	21.98 Å
Atom count	2726
Residues	330
Excluded volume	48758 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2d4g__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 (2)

▼

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2d4gA00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1140 — Cyclic Phosphodiesterase; Chain: A,
Homologous superfamily homologous superfamily	10 — Cyclic phosphodiesterase

Domain ID domain_id	2d4gB00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1140 — Cyclic Phosphodiesterase; Chain: A,
Homologous superfamily homologous superfamily	10 — Cyclic phosphodiesterase

▶

Unit-cell length a length_a	99.660 Å
Unit-cell length b length_b	73.930 Å
Unit-cell length c length_c	61.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2350
R_work r_work	0.2240
R_free r_free	0.2640

Description description	hypothetical protein BSU11850
Molecular weight formula_weight	19827.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2970

Structure of YjcG protein, a putative 2'-5' RNA ligase from Bacillus subtilis

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

hypothetical protein BSU11850

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

2d4g__assembly_1__model_1

2d4g__assembly_1__model_1 | I(q)

2d4g__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Source organism organism	Bacillus subtilis
NCBI taxonomy ID ncbi_taxonomy_id	1423
Host organism host_organism	Escherichia coli BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	244

Structure of YjcG protein, a putative 2'-5' RNA ligase from Bacillus subtilis

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

hypothetical protein BSU11850

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

2d4g__assembly_1__model_1

2d4g__assembly_1__model_1 | I(q)

2d4g__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)