SAXSdb — 1y69

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

50S ribosomal protein L16

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 Heteromer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain K； UniProt 1–141	Not recorded	23S ribosomal RNA × 1 5S ribosomal RNA × 1 50S ribosomal protein L27 × 1 （Q9RY65） Ribosome-recycling factor × 1 （P0A805）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.33 Å R-free 0.338

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 1Y69	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1NJM The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin Deposited 2003-01-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain K 2–142（141 aa）	Not recorded	SPS SPARSOMYCIN × 1	X-RAY DIFFRACTION X-ray crystallization conditions ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM	Resolution 3.60 Å R-free 0.308
1NJP The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) Deposited 2003-01-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain K 2–142（141 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM , pH 7.80	Resolution 3.50 Å R-free 0.295
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain K 1–140（140 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 construct 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 K 2–142（141 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 construct 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 K 2–142（141 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 construct 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 K 1–142（142 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 construct 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 K 2–142（141 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
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 J 1–141（141 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 1–141（141 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 J 5–140（136 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 J 5–140（136 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 J 1–141（141 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 J 1–141（141 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 J 5–140（136 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 J 5–140（136 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 J 5–138（134 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	RL16_DEIRA
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain K； PDBConstruct 1–141； UniProt 1–141

50S ribosomal protein L27

OrganismNot specified

UniProt Q9RY65

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 Heteromer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain U； UniProt 1–91	Not recorded	23S ribosomal RNA × 1 5S ribosomal RNA × 1 50S ribosomal protein L16 × 1 （Q9RXJ5） Ribosome-recycling factor × 1 （P0A805）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.33 Å R-free 0.338

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 1Y69	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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain U 1–91（91 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 U 1–91（91 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 U 1–91（91 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 U 1–91（91 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 U 1–91（91 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
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 T 1–91（91 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 experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric	Chain T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 1–91（91 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 T 2–85（84 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 T 2–85（84 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 T 1–91（91 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 T 1–91（91 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 T 12–85（74 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain T 1–91（91 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 T 12–83（72 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

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL27_DEIRA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain U； PDBConstruct 1–91； UniProt 1–91

Ribosome-recycling factor

Escherichia coli

UniProt P0A805

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 Heteromer Protein × 3 RNA 2 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain 8； UniProt 1–30 Chain 8； UniProt 106–185	Fragment：UNP residues 1-30 and 106-185 Mutation：RRF domain II deletion and GGG insertion	23S ribosomal RNA × 1 5S ribosomal RNA × 1 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L27 × 1 （Q9RY65）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 3.33 Å R-free 0.338

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 1Y69	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EK8 CRYSTAL STRUCTURE OF THE RIBOSOME RECYCLING FACTOR (RRF) FROM ESCHERICHIA COLI Deposited 2000-03-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–185（185 aa）	Not recorded	HG MERCURY (II) ION × 3 DEM DECYLOXY-METHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1 M MES-NaOH, 10 % PEG 350 MME, 12 % PEG 400, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 287K	Resolution 2.30 Å R-free 0.297
1ISE Crystal structure of a mutant of ribosome recycling factor from Escherichia coli, Arg132Gly Deposited 2001-11-30	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–185（185 aa）	Mutation：R132G	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；277 K；50mM MES-NaOH, PEG 1500, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.20 Å R-free 0.297
1ZN0 Coordinates of RRF and EF-G fitted into Cryo-EM map of the 50S subunit bound with both EF-G (GDPNP) and RRF Deposited 2005-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric	Chain A 1–185（185 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 15.50 Å
1ZN1 Coordinates of RRF fitted into Cryo-EM map of the 70S post-termination complex Deposited 2005-05-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–185（185 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 14.10 Å
2RDO 50S subunit with EF-G(GDPNP) and RRF bound Deposited 2007-09-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 34-meric	Chain 8 1–185（185 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer PolyMix；pH 7.5；PolyMix cryo-EM vitrification conditions Cryogen ETHANE；Rapid-freezing in liquid ethane by Vitrobot	Resolution 9.10 Å
4V9C Allosteric control of the ribosome by small-molecule antibiotics Deposited 2012-07-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric	Chain CY 1–185（185 aa）	Not recorded	MG MAGNESIUM ION × 266 NMY NEOMYCIN × 8 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；291 K；PEG800, MPD, pH 6.5, microbatch, temperature 291K	Resolution 3.30 Å R-free 0.255
4V9D Structures of the bacterial ribosome in classical and hybrid states of tRNA binding Deposited 2012-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric	Chain AY 2–183（182 aa）	Not recorded	MG MAGNESIUM ION × 271 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8000, MPD, pH 6.5, microbatch, temperature 291K	Resolution 3.00 Å R-free 0.260
4WOI 4,5-linked aminoglycoside antibiotics regulate the bacterial ribosome by targeting dynamic conformational processes within intersubunit bridge B2 Deposited 2014-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric	Chain AV 1–185（185 aa）	Not recorded	MG MAGNESIUM ION × 269 PAR PAROMOMYCIN × 6 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 6.5；291 K；PEG8k, MPD, KCl, KSCN	Resolution 3.00 Å R-free 0.253

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

View Construct and Data Evidence

UniProt name	RRF_ECOLI
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain 8； PDBConstruct 1–30； UniProt 1–30 Author chain 8； PDBConstruct 34–113； UniProt 106–185

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	1y69
Deposition date deposition_date	2004-12-04
Structure title title	RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans
Keywords keywords	RIBOSOME, 50S, RRF, RECYCLING FACTOR; 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	66.60 Å
Radius of gyration Rg (electron density) rg_electron	66.15 Å
Forward intensity I(0) i0	39929100000.00
Molecular weight molecular_weight	974710.0 kDa
Excluded volume excluded_volume	919080 Å³
Envelope volume envelope_volume	1765300 Å³
Hydration-shell volume shell_volume	208800 Å³
Envelope diameter envelope_diameter	248.8 Å
Shell Rg shell_rg	75.73 Å
Envelope Rg envelope_rg	65.71 Å
Shape Rg shape_rg	66.12 Å
Total Rg total_rg	66.27 Å
Total atoms total_atoms	64484
Residues n_residues	3217
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	257.5 Å
Rg (real space) rg_real	70.19 Å
Rg uncertainty (real space) rg_real_error	1.70 Å
I(0) (real space) i0_real	4.0200e+10
I(0) uncertainty (real space) i0_real_error	8.3630e+08
Rg (reciprocal space) rg_reciprocal	66.86 Å
I(0) (reciprocal space) i0_reciprocal	39970000000.0000
Solution quality estimate total_estimate	0.8546
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	85.8 Å
Skewness Skewness skewness	0.676
Kurtosis Kurtosis kurtosis	0.700
Angular range angular_range	— – 0.1200 Å⁻¹
Current regularization parameter α current_alpha	0.8338
Highest regularization parameter α highest_alpha	5163000000.0000
Real-space data points n_real_points	25
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.548; Stabil: 0.864; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.902

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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	64484

GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

Entity 2 Entity 2 polymer

Description description	5S ribosomal RNA
Molecular weight formula_weight	39911.9 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	9

ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU

Entity 3 Entity 3 polymer

Description description	50S ribosomal protein L16
Molecular weight formula_weight	16126.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MLLPKRTKFRKQFRGRMTGDAKGGDYVAFGDYGLIAMEPAWIKSNQIEACRIVMSRHFRRGGKIYIRIFPDKPVTKKPAETRMGKGKGAVEYWVSVVKPGRVMFEVAGVTEEQAKEAFRLAGHKLPIQTKMVKREVYDEAQ

Entity 4 Entity 4 polymer

Description description	50S ribosomal protein L27
Molecular weight formula_weight	9609.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U

MAHKKGVGSSKNGRDSNPKYLGVKKFGGEVVKAGNILVRQRGTKFKAGQGVGMGRDHTLFALSDGKVVFINKGKGARFISIEAAQTEVAAD

Entity 5 Entity 5 polymer

Description description	Ribosome-recycling factor
Molecular weight formula_weight	12844.6 kDa
Mutation mutation	RRF domain II deletion and GGG insertion
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	8

MISDIRKDAEVRMDKCVEAFKTQISKIRTGGGGTEERRKDLTKIVRGEAEQARVAVRNVRRDANDKVKALLKDKEISEDDDRRSQDDVQKLTDAAIKKIEAALADKEAELMQF

来源 Source

来源生物 organism	Escherichia coli
NCBI Class编号 ncbi_taxonomy_id	83333
宿主生物 host_organism	Escherichia coli

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1y69k1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamily	d.41.4 — Ribosomal protein L16p/L10e
Family Family family	d.41.4.2 — Ribosomal protein L16p

Domain ID domain_id	d1y69u1
Class class	b — All beta proteins
Fold Fold fold	b.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamily	b.84.4 — Ribosomal L27 protein-like
Family Family family	b.84.4.1 — Ribosomal L27 protein

CATH v4.4 (3 domains)

Domain ID domain_id	1y69800
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	20 — Ribosome-recycling factor

Domain ID domain_id	1y69K01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily	10 — Ribosomal protein L16/L10

Domain ID domain_id	1y69U01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	100 — RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain

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8. Citations (1)

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Unit-cell length a length_a	168.700 Å
Unit-cell length b length_b	405.000 Å
Unit-cell length c length_c	693.000 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	8

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

Resolution resolution	3.330 Å
Low-resolution limit resolution_low	8.130 Å
R factor r_factor	0.2750
R_work r_work	0.2750
R_free r_free	0.3380

fit	/app/data/saxs_computation/y6/1y69/1y69.fit
pddf	/app/data/pr_computation/y6/1y69/1y69.pr.out
profile	/app/data/saxs_computation/y6/1y69/1y69.dat

RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans

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

50S ribosomal protein L16

State in the Current Structure

Other States of the Same Protein in the Database

50S ribosomal protein L27

State in the Current Structure

Other States of the Same Protein in the Database

Ribosome-recycling factor

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

CATH v4.4 (3 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)