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	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 58–133	Fragment：C-Terminal Domain Of Ribosomal Protein L11 Mutation：S69N	58 Nucleotide Ribosomal 23S RNA Domain × 1 3CO COBALT (III) ION × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 10 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；310 K；PEG600, Magnesium acetate, glycerol, sodium cacodylate, potasium chlroride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K	Resolution 2.80 Å R-free 0.253
2	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain B； UniProt 58–133	Fragment：C-Terminal Domain Of Ribosomal Protein L11 Mutation：S69N	58 Nucleotide Ribosomal 23S RNA Domain × 1 3CO COBALT (III) ION × 1 K POTASSIUM ION × 1 MG MAGNESIUM ION × 8 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；310 K；PEG600, Magnesium acetate, glycerol, sodium cacodylate, potasium chlroride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 310K	Resolution 2.80 Å R-free 0.253

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1Y39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ACI L11 RIBOSOMAL PROTEIN RNA BINDING DOMAIN, NMR, 20 STRUCTURES Deposited 1997-02-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：C-TERMINAL DOMAIN, 76 RESIDUES	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K	Resolution not provided
1C04 IDENTIFICATION OF KNOWN PROTEIN AND RNA STRUCTURES IN A 5 A MAP OF THE LARGE RIBOSOMAL SUBUNIT FROM HALOARCULA MARISMORTUI Deposited 1999-07-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 63–129（67 aa） Fragment：C-TERMINAL DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；292 K；PEG 6000, POTASSIUM CHLORIDE, AMMONIUM CHLORIDE, MAGNESIUM CHLORIDE, ACETATE, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 5.00 Å
1FOW NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF 50S RIBOSOMAL PROTEIN L11, MINIMIZED AVERAGE STRUCTURE Deposited 1996-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：CARBOXYL-TERMINAL DOMAIN OF PROTEIN L11, RESIDUES THR 59 TO ASP 133	Mutation：INS(MET1)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K	Resolution not provided
1FOX NMR STRUCTURE OF L11-C76, THE C-TERMINAL DOMAIN OF 50S RIBOSOMAL PROTEIN L11, 33 STRUCTURES Deposited 1996-09-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：CARBOXYL-TERMINAL DOMAIN OF PROTEIN L11, RESIDUES THR 59 TO ASP 133	Mutation：INS(MET1)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K	Resolution not provided
1FOY THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：C-TERMINAL DOMAIN, 75 RESIDUES	Mutation：F1M	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；320 K	Resolution not provided
1HC8 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 2001-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 58–133（76 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 10 K POTASSIUM ION × 1 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50	Resolution 2.80 Å R-free 0.253
1HC8 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 2001-04-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 58–133（76 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 11 K POTASSIUM ION × 1 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50	Resolution 2.80 Å R-free 0.253
1QA6 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 1999-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 63–129（67 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 2 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；310 K；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 310.00K	Resolution 2.80 Å R-free 0.321
1QA6 CRYSTAL STRUCTURE OF A CONSERVED RIBOSOMAL PROTEIN-RNA COMPLEX Deposited 1999-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 63–129（67 aa） Fragment：C-TERMINAL DOMAIN OF RIBOSOMAL PROTEIN L11	Not recorded	MG MAGNESIUM ION × 2 OS OSMIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；310 K；PEG 600, MAGNESIUM ACETATE, COBALT HEXAMINE CHLORIDE, SODIUM CACODYLATE, KCL, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 310.00K	Resolution 2.80 Å R-free 0.321
2FOW THE RNA BINDING DOMAIN OF RIBOSOMAL PROTEIN L11: THREE-DIMENSIONAL STRUCTURE OF THE RNA-BOUND FORM OF THE PROTEIN, NMR, 26 STRUCTURES Deposited 1997-05-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 59–133（75 aa） Fragment：C-TERMINAL DOMAIN, 75 RESIDUES	Mutation：F1M	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；320 K	Resolution not provided

8 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

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. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.99 Å
Radius of gyration Rg (electron density) rg_electron	25.51 Å
Forward intensity I(0) i0	109724000.00
Molecular weight molecular_weight	54337.0 kDa
Excluded volume excluded_volume	55602 Å³
Envelope volume envelope_volume	76153 Å³
Hydration-shell volume shell_volume	25794 Å³
Envelope diameter envelope_diameter	93.5 Å
Shell Rg shell_rg	31.71 Å
Envelope Rg envelope_rg	25.33 Å
Shape Rg shape_rg	25.47 Å
Total Rg total_rg	26.00 Å
Total atoms total_atoms	3617
Residues n_residues	260
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	89.6 Å
Rg (real space) rg_real	26.08 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	1.0970e+08
I(0) uncertainty (real space) i0_real_error	1.7070e+06
Rg (reciprocal space) rg_reciprocal	26.05 Å
I(0) (reciprocal space) i0_reciprocal	109700000.0000
Solution quality estimate total_estimate	0.8725
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.433
Kurtosis Kurtosis kurtosis	-0.262
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6058000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.834; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.890; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. 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

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 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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7. 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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8. Citations (1)

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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

fit	/app/data/saxs_computation/y3/1y39/1y39.fit
pddf	/app/data/pr_computation/y3/1y39/1y39.pr.out
profile	/app/data/saxs_computation/y3/1y39/1y39.dat

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 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

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)