SAXSdb — 1r2x

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

50S ribosomal protein L11

OrganismNot specified

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 1–140	Not recorded	58nts of 23S rRNA × 1	ELECTRON MICROSCOPY cryo-EM buffer：Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions：Cryogen ETHANE；Rapid freezing in liquid ethane	Resolution 9.00 Å

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 1R2X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain K 1–140（140 aa）	Not recorded	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
1JQM Fitting of L11 protein and elongation factor G (EF-G) in the cryo-em map of e. coli 70S ribosome bound with EF-G, GDP and fusidic acid Deposited 2001-08-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6	Resolution 18.00 Å
1JQS Fitting of L11 protein and elongation factor G (domain G' and V) in the cryo-em map of E. coli 70S ribosome bound with EF-G and GMPPCP, a nonhydrolysable GTP analog Deposited 2001-08-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1JQT Fitting of L11 protein in the low resolution cryo-EM map of E.coli 70S ribosome Deposited 2001-08-07	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–139（139 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 18.00 Å
1MMS Crystal structure of the ribosomal PROTEIN L11-RNA complex Deposited 1999-04-14	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–140（140 aa）	Not recorded	CD CADMIUM ION × 5 MG MAGNESIUM ION × 10 MMC METHYL MERCURY ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.254
1MMS Crystal structure of the ribosomal PROTEIN L11-RNA complex Deposited 1999-04-14	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–140（140 aa）	Not recorded	CD CADMIUM ION × 3 MG MAGNESIUM ION × 9 MMC METHYL MERCURY ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.3；277 K；25% GLYCEROL, 15% PEG 4000, 50 MM TRIS PH 7.5, 50 MM MGCL2, 20 MM CDCL2, 0.2 M KCL, 1 MM DITHIOTHREITOL, 4 DEGREES C, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.57 Å R-free 0.254
1MVR Decoding Center & Peptidyl transferase center from the X-ray structure of the Thermus thermophilus 70S ribosome, aligned to the low resolution Cryo-EM map of E.coli 70S Ribosome Deposited 2002-09-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: octameric	Chain L 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer polymix buffer；pH 7.5；polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 12.80 Å
1OLN Model for thiostrepton antibiotic binding to L11 substrate from 50S ribosomal RNA Deposited 2003-08-08	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 2–141（140 aa）	Not recorded	No recorded non-water small molecule	Experimental method not declared NMR measurement conditions pH 6.2；303 K；Ionic strength (raw mmCIF value) 100 MM NACL, 5 MM MGCL2；Pressure 1	Resolution not provided
1PN7 Coordinates of S12, L11 proteins and P-tRNA, from the 70S X-ray structure aligned to the 70S Cryo-EM map of E.coli ribosome Deposited 2003-06-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain L 7–139（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
1PN8 Coordinates of S12, L11 proteins and E-site tRNA from 70S crystal structure separately fitted into the Cryo-EM map of E.coli 70S.EF-G.GDPNP complex. The atomic coordinates originally from the E-site tRNA were fitted in the position of the hybrid P/E-site tRNA. Deposited 2003-06-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain L 7–139（133 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane	Resolution 10.80 Å
1R2W Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of the 70S ribosome Deposited 2003-09-30	Parsed fields agree	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–140（140 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer Polymix buffer；pH 7.5；Polymix buffer cryo-EM vitrification conditions Cryogen ETHANE；Rapid freezing in liquid ethane	Resolution 9.00 Å
2BCW Coordinates of the N-terminal domain of ribosomal protein L11,C-terminal domain of ribosomal protein L7/L12 and a portion of the G' domain of elongation factor G, as fitted into cryo-em map of an Escherichia coli 70SEF-GGDP*fusidic acid complex Deposited 2005-10-19	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 7–71（65 aa） Fragment：N-terminal domain	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer 20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine；pH 7.5；20mM HEPES-KOH (pH 7.5), 6mM MgCl2, and 150 mM NH4Cl, 2mM spermidine, 0.4 mM spermine cryo-EM vitrification conditions RAPID-FREEZING IN LIQUID ETHANE	Resolution 11.20 Å
2JQ7 Model for thiostrepton binding to the ribosomal L11-RNA Deposited 2007-05-30	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 220；Pressure 1 NMR sample composition 0.3 MM [U-13C, U-15N U-2H] RIBOSOMAL PROTEIN L11, 0.3 MM RIBOSOMAL RNA, 0.3 MM THIOSTREPTON ANTIBIOTIC, 20 MM POTASSIUM PHOSPHATE, 200 MM POTASSIUM CHLORIDE, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2K3F Ribosomal protein L11 from Thermotoga maritima Deposited 2008-05-06	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–141（141 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.1；298 K；Ionic strength (raw mmCIF value) 70；Pressure ambient NMR sample composition 1.2 mM [U-100% 15N] L11, 20 mM potassium phosphate, 50 mM potassium chloride, 10 % [U-100% 2H] D2O, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
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 conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain L 8–140（133 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 construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BL 1–141（141 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å

15 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL11_THEMA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–141； UniProt 1–140

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	1r2x
Deposition date deposition_date	2003-09-30
Structure title title	Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome
Keywords keywords	rna, ribosomal protein, RNA BINDING PROTEIN-RNA COMPLEX; RNA BINDING PROTEIN/RNA
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	20.77 Å
Radius of gyration Rg (electron density) rg_electron	19.31 Å
Forward intensity I(0) i0	6886920.00
Molecular weight molecular_weight	16041.0 kDa
Excluded volume excluded_volume	18127 Å³
Envelope volume envelope_volume	23193 Å³
Hydration-shell volume shell_volume	11121 Å³
Envelope diameter envelope_diameter	62.5 Å
Shell Rg shell_rg	23.21 Å
Envelope Rg envelope_rg	18.57 Å
Shape Rg shape_rg	19.87 Å
Total Rg total_rg	19.80 Å
Total atoms total_atoms	57
Residues n_residues	57
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	61.2 Å
Rg (real space) rg_real	20.66 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	6.8870e+06
I(0) uncertainty (real space) i0_real_error	7.5360e+04
Rg (reciprocal space) rg_reciprocal	20.68 Å
I(0) (reciprocal space) i0_reciprocal	6887000.0000
Solution quality estimate total_estimate	0.8661
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.4 Å
Skewness Skewness skewness	0.035
Kurtosis Kurtosis kurtosis	-0.663
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1339000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.367

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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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1r2xa_
Class class	i — Low resolution protein structures
Fold Fold fold	i.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamily	i.1.1 — Ribosome and ribosomal fragments
Family Family family	i.1.1.1 — Ribosome complexes

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	9.00 Å
Resolution测定方法 resolution_method	Reference based alignment
颗粒数 num_particles	75996

Description description	58nts of 23S rRNA
Molecular weight formula_weight	18693.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer type type	polyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	190

Coordinates of L11 with 58nts of 23S rRNA fitted into the cryo-EM map of EF-Tu ternary complex (GDP.Kirromycin) bound 70S ribosome

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/r2/1r2x/1r2x.fit
pddf	/app/data/pr_computation/r2/1r2x/1r2x.pr.out
profile	/app/data/saxs_computation/r2/1r2x/1r2x.dat