SAXSdb — 1rl6

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

PROTEIN (RIBOSOMAL PROTEIN L6)

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–177	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.6；pH 7.6	Resolution 2.00 Å R-free 0.302

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 1RL6	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain B 1–177（177 aa）	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
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain J 1–171（171 aa）	Mutation：B. STEAROTHERMOPHILUS SEQUENCE AND MODEL	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain J 8–171（164 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BH 1–177（177 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL6_BACST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–177； UniProt 1–177

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	1rl6
Deposition date deposition_date	1999-01-14
Structure title title	RIBOSOMAL PROTEIN L6
Keywords keywords	RNA-BINDING PROTEIN, GENTAMICIN RESISTANCE, RIBOSOMAL PROTEIN, ALPHA/BETA PROTEIN, RNA BINDING PROTEIN; RNA BINDING PROTEIN
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	21.24 Å
Radius of gyration Rg (electron density) rg_electron	20.59 Å
Forward intensity I(0) i0	5793550.00
Molecular weight molecular_weight	17770.0 kDa
Excluded volume excluded_volume	22402 Å³
Envelope volume envelope_volume	27933 Å³
Hydration-shell volume shell_volume	12711 Å³
Envelope diameter envelope_diameter	69.0 Å
Shell Rg shell_rg	24.63 Å
Envelope Rg envelope_rg	20.67 Å
Shape Rg shape_rg	20.61 Å
Total Rg total_rg	21.21 Å
Total atoms total_atoms	1251
Residues n_residues	164
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	70.5 Å
Rg (real space) rg_real	21.45 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	5.7940e+06
I(0) uncertainty (real space) i0_real_error	7.4110e+04
Rg (reciprocal space) rg_reciprocal	21.41 Å
I(0) (reciprocal space) i0_reciprocal	5793000.0000
Solution quality estimate total_estimate	0.8224
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.6 Å
Skewness Skewness skewness	0.438
Kurtosis Kurtosis kurtosis	-0.643
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1137000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.740; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.605; Smooth: 0.863

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rl6a1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.141 — Ribosomal protein L6
Superfamily Superfamily superfamily	d.141.1 — Ribosomal protein L6
Family Family family	d.141.1.1 — Ribosomal protein L6

Domain ID domain_id	d1rl6a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.141 — Ribosomal protein L6
Superfamily Superfamily superfamily	d.141.1 — Ribosomal protein L6
Family Family family	d.141.1.1 — Ribosomal protein L6

CATH v4.4 (2 domains)

Domain ID domain_id	1rl6A01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily	12 — Ribosomal protein L6

Domain ID domain_id	1rl6A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily	12 — Ribosomal protein L6

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8. Citations (2)

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Unit-cell length a length_a	71.800 Å
Unit-cell length b length_b	71.800 Å
Unit-cell length c length_c	124.500 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2570
R_free r_free	0.3020

Description description	PROTEIN (RIBOSOMAL PROTEIN L6)
Molecular weight formula_weight	19202.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1391

RIBOSOMAL PROTEIN L6

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

PROTEIN (RIBOSOMAL PROTEIN L6)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 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	140

fit	/app/data/saxs_computation/rl/1rl6/1rl6.fit
pddf	/app/data/pr_computation/rl/1rl6/1rl6.pr.out
profile	/app/data/saxs_computation/rl/1rl6/1rl6.dat