SAXSdb — 1y39

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

50S ribosomal protein L11

Geobacillus stearothermophilus

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	58 Nucleotide Ribosomal 23S RNA Domain × 1 COBALT (III) ION × 1 POTASSIUM ION × 1 MAGNESIUM ION × 10 GLYCEROL × 1 water × 2	Consistent with all polymers
2	Protein–RNA	Monomer	Protein 1 RNA 1	58 Nucleotide Ribosomal 23S RNA Domain × 1 COBALT (III) ION × 1 POTASSIUM ION × 1 MAGNESIUM ION × 8 GLYCEROL × 1 water × 2	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RL11_BACST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 58–133 Author chain B； PDBConstruct 1–76； UniProt 58–133

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	1y39
Deposition date deposition_date	2004-11-24
Structure title title	Co-evolution of protein and RNA structures within a highly conserved ribosomal domain
Keywords keywords	X-Ray Crystal structure, Choroplast-Like L11 complex, rRNA, 23S RNA, STRUCTURAL PROTEIN-RNA COMPLEX; STRUCTURAL PROTEIN/RNA
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.

1y39__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1y39__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1y39__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	18.41 Å
Rg (electron density)	18.22 Å
Total Rg	18.80 Å
Atom count	1800
Residues	129
Excluded volume	27619 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1y39__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1y39__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	58 Nucleotide Ribosomal 23S RNA Domain
Molecular weight formula_weight	18863.1 kDa
Mutation mutation	G1062U, C1076A
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C,D
Atom count atom_count	3632

GCCAGGAUGUAUGCUUAGAAGCAGCAAUCAUUUAAAGAGUGCGUAAUAGCUCACUGGU

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L11
Molecular weight formula_weight	8195.6 kDa
Mutation mutation	S69N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

FTFITKTPPAAVLLKKAAGIESGSGEPNRNKVATIKRDKVREIAELKMPDLNAASIEAAMRMIEGTARNMGIVVED

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	Escherichia coli BL21

Entity 3 Entity 3 non-polymer

Description description	COBALT (III) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	POTASSIUM ION
Molecular weight formula_weight	39.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 6 Entity 6 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	15

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1y39a1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.7 — Ribosomal protein L11, C-terminal domain
Family Family family	a.4.7.1 — Ribosomal protein L11, C-terminal domain

Domain ID domain_id	d1y39b1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.7 — Ribosomal protein L11, C-terminal domain
Family Family family	a.4.7.1 — Ribosomal protein L11, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	1y39A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	250 — Ribosomal protein L11/L12, C-terminal domain

Domain ID domain_id	1y39B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	250 — Ribosomal protein L11/L12, C-terminal domain

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Unit-cell length a length_a	150.240 Å
Unit-cell length b length_b	150.240 Å
Unit-cell length c length_c	62.984 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	16

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	18.000 Å
R factor r_factor	0.2200
R_work r_work	0.2200
R_free r_free	0.2530

Co-evolution of protein and RNA structures within a highly conserved ribosomal domain

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

50S ribosomal protein L11

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

1y39__assembly_2__model_1

1y39__assembly_2__model_1 | I(q)

1y39__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Co-evolution of protein and RNA structures within a highly conserved ribosomal domain

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

50S ribosomal protein L11

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

1y39__assembly_2__model_1

1y39__assembly_2__model_1 | I(q)

1y39__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)