SAXSdb — 2ogo

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

50S ribosomal protein L3

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 B； UniProt 1–211	Not recorded	23S ribosomal RNA × 1 G34 Retapamulin × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.66 Å R-free 0.334

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 2OGO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP	Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	773 CETHROMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	ZIT AZITHROMYCIN × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric	Chain B 1–211（211 aa）	Not recorded	DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K	Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	MUL TIAMULIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K	Resolution 3.50 Å R-free 0.360
2OGM The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519 Deposited 2007-01-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–211（211 aa）	Not recorded	G19 (2S,3AR,4R,5S,6S,8R,9R,9AR,10R)-2,5-DIHYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROP[1]ENOCYCLOPENTA[8]ANNULEN-8-YL [(6-AMINOPYRIDAZIN-3-YL)CARBONYL]CARBAMATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.50 Å R-free 0.334
2OGN The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080 Deposited 2007-01-07	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain B 1–211（211 aa）	Not recorded	G80 (3AS,4R,5S,6S,8R,9R,9AR,10R)-5-HYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROPANOCYCLOPENTA[8]ANNULEN-8-YL (PIPERIDIN-4-YLTHIO)ACETATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.56 Å R-free 0.338
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP	Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 35	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP	Resolution 3.30 Å R-free 0.318
3DLL The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning Deposited 2008-06-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP	Resolution 3.50 Å R-free 0.280
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.	Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.	Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 51	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol	Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain B 1–211（211 aa）	Not recorded	MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol	Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–205（205 aa）	Not recorded	MG MAGNESIUM ION × 198	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol	Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric	Chain B 1–205（205 aa）	Not recorded	MG MAGNESIUM ION × 186 HGR Hygromycin A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol	Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric	Chain B 1–211（211 aa）	Not recorded	6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.	Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain B 1–211（211 aa）	Not recorded	6O1 Evernimicin × 1 MG MAGNESIUM ION × 123	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol	Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain B 1–206（206 aa）	Not recorded	QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.	Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain B 1–206（206 aa）	Not recorded	QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.	Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain B 1–206（206 aa）	Not recorded	MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.	Resolution 3.40 Å R-free 0.318

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL3_DEIRA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–211； UniProt 1–211

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	2ogo
Deposition date deposition_date	2007-01-07
Structure title title	The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)
Keywords keywords	retapamulin, SB-275833, pleuromutilin, PTC, peptidyl transferase center, ribosome, antibiotic; RIBOSOME
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	65.49 Å
Radius of gyration Rg (electron density) rg_electron	65.12 Å
Forward intensity I(0) i0	36134900000.00
Molecular weight molecular_weight	921500.0 kDa
Excluded volume excluded_volume	864470 Å³
Envelope volume envelope_volume	1676400 Å³
Hydration-shell volume shell_volume	201720 Å³
Envelope diameter envelope_diameter	249.1 Å
Shell Rg shell_rg	74.72 Å
Envelope Rg envelope_rg	64.41 Å
Shape Rg shape_rg	64.95 Å
Total Rg total_rg	65.43 Å
Total atoms total_atoms	59372
Residues n_residues	2765
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	214.4 Å
Rg (real space) rg_real	65.12 Å
Rg uncertainty (real space) rg_real_error	1.41 Å
I(0) (real space) i0_real	3.6130e+10
I(0) uncertainty (real space) i0_real_error	7.7730e+08
Rg (reciprocal space) rg_reciprocal	65.77 Å
I(0) (reciprocal space) i0_reciprocal	36170000000.0000
Solution quality estimate total_estimate	0.8569
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	80.4 Å
Skewness Skewness skewness	0.253
Kurtosis Kurtosis kurtosis	-0.273
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3388000000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.822; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.728

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	933405.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	0
Atom count atom_count	59577

GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Entity 2 Entity 2 polymer

Description description	50S ribosomal protein L3
Molecular weight formula_weight	22477.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKASAAKGGK

Entity 3 Entity 3 non-polymer

Description description	Retapamulin
Molecular weight formula_weight	517.8 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2ogob1
Class class	b — All beta proteins
Fold Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamily	b.43.3 — Translation proteins
Family Family family	b.43.3.2 — Ribosomal protein L3

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8. Citations (1)

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Unit-cell length a length_a	170.115 Å
Unit-cell length b length_b	405.873 Å
Unit-cell length c length_c	695.243 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	3.660 Å
Low-resolution limit resolution_low	29.960 Å
R factor r_factor	—
R_work r_work	0.2600
R_free r_free	0.3340

fit	/app/data/saxs_computation/og/2ogo/2ogo.fit
pddf	/app/data/pr_computation/og/2ogo/2ogo.pr.out
profile	/app/data/saxs_computation/og/2ogo/2ogo.dat

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833)

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

50S ribosomal protein L3

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-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)