SAXSdb — 2ogn

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1. 蛋白身份与相关结构 Protein Identity & Related Structures

50S ribosomal protein L3

物种未注明

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白–RNA 单体蛋白 × 1 RNA 1 PDB 声明：dimeric（2）与全部聚合物数一致	链 B； UniProt 1–211	未记录	23S ribosomal RNA × 1 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结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 3.56 Å R-free 0.338

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 2OGN	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans 提交 2003-01-05	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP	分辨率 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 提交 2003-02-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	773 CETHROMYCIN × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K	分辨率 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN 提交 2003-02-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	ZIT AZITHROMYCIN × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN 提交 2004-03-08	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 30 PDB 声明：32-meric	链 B 1–211（211 aa）	未记录	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结晶条件 pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K	分辨率 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 提交 2004-08-31	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	MUL TIAMULIN × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K	分辨率 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 提交 2007-01-07	配体/离子不同结构质量不同	Assembly 1 蛋白–RNA 单体；蛋白 × 1 PDB 声明：dimeric	链 B 1–211（211 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 3.50 Å R-free 0.334
2OGO The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833) 提交 2007-01-07	配体/离子不同结构质量不同	Assembly 1 蛋白–RNA 单体；蛋白 × 1 PDB 声明：dimeric	链 B 1–211（211 aa）	未记录	G34 Retapamulin × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K	分辨率 3.66 Å R-free 0.334
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans 提交 2008-03-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP	分辨率 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit 提交 2008-03-08	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	分辨率 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans 提交 2008-03-08	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	MG MAGNESIUM ION × 35	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	分辨率 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans 提交 2008-03-02	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 29 PDB 声明：31-meric	链 B 1–211（211 aa）	未记录	MG MAGNESIUM ION × 36	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP	分辨率 3.30 Å R-free 0.318
3DLL The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning 提交 2008-06-27	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP	分辨率 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 提交 2010-11-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.	分辨率 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 提交 2010-11-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.	分辨率 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans 提交 2013-01-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	分辨率 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans 提交 2013-01-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	分辨率 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans 提交 2013-01-07	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–211（211 aa）	未记录	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结晶条件 VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP	分辨率 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 提交 2014-07-28	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 26 PDB 声明：28-meric	链 B 1–211（211 aa）	未记录	MG MAGNESIUM ION × 51	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol	分辨率 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 提交 2014-09-16	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 26 PDB 声明：28-meric	链 B 1–211（211 aa）	未记录	MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol	分辨率 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans 提交 2015-09-08	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–205（205 aa）	未记录	MG MAGNESIUM ION × 198	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol	分辨率 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A 提交 2015-09-08	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 28 PDB 声明：30-meric	链 B 1–205（205 aa）	未记录	MG MAGNESIUM ION × 186 HGR Hygromycin A × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol	分辨率 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin 提交 2016-05-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 27 PDB 声明：29-meric	链 B 1–211（211 aa）	未记录	6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin 提交 2016-05-11	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 26 PDB 声明：28-meric	链 B 1–211（211 aa）	未记录	6O1 Evernimicin × 1 MG MAGNESIUM ION × 123	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol	分辨率 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I 提交 2020-08-10	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 26 PDB 声明：28-meric	链 B 1–206（206 aa）	未记录	QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I 提交 2020-08-10	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 26 PDB 声明：28-meric	链 B 1–206（206 aa）	未记录	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结晶条件 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.	分辨率 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV 提交 2020-08-12	构建体不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白–RNA 异源复合物；蛋白 × 26 PDB 声明：28-meric	链 B 1–206（206 aa）	未记录	MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 3.40 Å R-free 0.318

共 26 个其他 PDB 条目、26 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	RL3_DEIRA
Isoform	—
PDB实体	2
链与序列区间	作者链 B； PDB构建体 1–211； UniProt 1–211

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	2ogn
沉积日期 deposition_date	2007-01-07
结构标题 title	The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080
关键词 keywords	SB-280080, pleuromutilin, PTC, peptidyl transferase center, ribosome, antibiotic; RIBOSOME
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	65.57 Å
回转半径 Rg (电子) rg_electron	65.20 Å
零角强度 I(0) i0	36164500000.00
分子量 molecular_weight	921800.0 kDa
排除体积 excluded_volume	864710 Å³
包络体积 envelope_volume	1684400 Å³
水化壳体积 shell_volume	202280 Å³
包络直径 envelope_diameter	250.5 Å
壳层 Rg shell_rg	74.77 Å
包络 Rg envelope_rg	64.63 Å
形状 Rg shape_rg	65.03 Å
总 Rg total_rg	65.51 Å
总原子数 total_atoms	59392
残基数 n_residues	2766
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	216.6 Å
Rg (实空间) rg_real	65.20 Å
Rg 误差 (实空间) rg_real_error	1.53 Å
I(0) (实空间) i0_real	3.6160e+10
I(0) 误差 (实空间) i0_real_error	7.5440e+08
Rg (倒空间) rg_reciprocal	65.86 Å
I(0) (倒空间) i0_reciprocal	36200000000.0000
解质量估计 total_estimate	0.8573
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	81.2 Å
偏度 Skewness skewness	0.253
峰度 Kurtosis kurtosis	-0.273
角度范围 angular_range	— – 0.1200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	3495000000.0000
实空间数据点数 n_real_points	25
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.807; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.947; Smooth: 0.774

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5. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	23S ribosomal RNA
分子量 formula_weight	933405.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polyribonucleotide
链编号 strand_id	0
原子数 atom_count	59597

GGUCAAGAUAGUAAGGGUCCACGGUGGAUGCCCUGGCGCUGGAGCCGAUGAAGGACGCGAUUACCUGCGAAAAGCCCCGACGAGCUGGAGAUACGCUUUGACUCGGGGAUGUCCGAAUGGGGAAACCCACCUCGUAAGAGGUAUCCGCAAGGAUGGGAACUCAGGGAACUGAAACAUCUCAGUACCUGAAGGAGAAGAAAGAGAAUUCGAUUCCGUUAGUAGCGGCGAGCGAACCCGGAUCAGCCCAAACCGAAACGCUUGCGUUUCGGGGUUGUAGGACCAGUUUUUAAGAUUCAACCCCUCAAGCCGAAGUGGCUGGAAAGCUACACCUCAGAAGGUGAGAGUCCUGUAGGCGAACGAGCGGUUGACUGUACUGGCACCUGAGUAGGUCGUUGUUCGUGAAACGAUGACUGAAUCCGCGCGGACCACCGCGCAAGGCUAAAUACUCCCAGUGACCGAUAGCGCAUAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAGAGAACCUGAAACCGUGGACUUACAAGCAGUCAUGGCACCUUAUGCGUGUUAUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUUAGACCUGACGUGCGAGCUUAAGUUGAAAAACGGAGGCGGAGCGAAAGCGAGUCCGAAUAGGGCGGCAUUAGUACGUCGGGCUAGACUCGAAACCAGGUGAGCUAAGCAUGACCAGGUUGAAACCCCCGUGACAGGGGGCGGAGGACCGAACCGGUGCCUGCUGAAACAGUCUCGGAUGAGUUGUGUUUAGGAGUGAAAAGCUAACCGAACCUGGAGAUAGCUAGUUCUCCCCGAAAUGUAUUGAGGUACAGCCUCGGAUGUUGACCAUGUCCUGUAGAGCACUCACAAGGCUAGGGGGCCUACCAGCUUACCAAACCUUAUGAAACUCCGAAGGGGCACGCGUUUAGUCCGGGAGUGAGGCUGCGAGAGCUAACUUCCGUAGCCGAGAGGGAAACAACCCAGACCAUCAGCUAAGGUCCCUAAAUGAUCGCUCAGUGGUUAAGGAUGUGUCGUCGCAUAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCACCCUUCAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGACGAUGCGCCGAAAAUGAUCGGGGCUCAAGUGAUCUACCGAAGCUAUGGAUUCAACUCGCGAAGCGAGUUGUCUGGUAGGGGAGCGUUCAGUCCGCGGAGAAGCCAUACCGGAAGGAGUGGUGGAGCCGACUGAAGUGCGGAUGCCGGCAUGAGUAACGAUAAAAGAAGUGAGAAUCUUCUUCGCCGUAAGGACAAGGGUUCCUGGGGAAGGGUCGUCCGCCCAGGGAAAGUCGGGACCUAAGGUGAGGCCGAACGGCGCAGCCGAUGGACAGCAGGUCAAGAUUCCUGCACCGAUCAUGUGGAGUGAUGGAGGGACGCAUUACGCUAUCCAAUGCCAAGCUAUGGCUAUGCUGGUUGGUACGCUCAAGGGCGAUCGGGUCAGAAAAUCUACCGGUCACAUGCCUCAGACGUAUCGGGAGCUUCCUCGGAAGCGAAGUUGGAAACGCGACGGUGCCAAGAAAAGCUUCUAAACGUUGAAACAUGAUUGCCCGUACCGCAAACCGACACAGGUGUCCGAGUGUCAAUGCACUAAGGCGCGCGAGAGAACCCUCGUUAAGGAACUUUGCAAUCUCACCCCGUAACUUCGGAAGAAGGGGUCCCCACGCUUCGCGUGGGGCGCAGUGAAUAGGCCCAGGCGACUGUUUACCAAAAUCACAGCACUCUGCCAACACGAACAGUGGACGUAUAGGGUGUGACGCCUGCCCGGUGCCGGAAGGUCAAGUGGAGCGGUGCAAGCUGCGAAAUGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAGGCGUAACGAUCUGGGCGCUGUCUCAACGAGGGACUCGGUGAAAUUGAAUUGGCUGUAAAGAUGCGGCCUACCCGUAGCAGGACGAAAAGACCCCGUGGAGCUUUACUAUAGUCUGGCAUUGGGAUUCGGGUUUCUCUGCGUAGGAUAGGUGGGAGCCUGCGAAACUGGCCUUUUGGGGUCGGUGGAGGCAACGGUGAAAUACCACCCUGAGAAACUUGGAUUUCUAACCUGAAAAAUCACUUUCGGGGACCGUGCUUGGCGGGUAGUUUGACUGGGGCGGUCGCCUCCCAAAAUGUAACGGAGGCGCCCAAAGGUCACCUCAAGACGGUUGGAAAUCGUCUGUAGAGCGCAAAGGUAGAAGGUGGCUUGACUGCGAGACUGACACGUCGAGCAGGGAGGAAACUCGGGCUUAGUGAACCGGUGGUACCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGAGUCCAUAUCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCUACGGGCGCAGGAGAAUUGAGGGGAGUUGCUCCUAGUACGAGAGGACCGGAGUGAACGGACCGCUGGUCUCCCUGCUGUCGUACCAACGGCACAUGCAGGGUAGCUAUGUCCGGAACGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCAGCCCCAAGAUGAGUUCUCCCACUGUUUAUCAGGUAAGACUCCCGGAAGACCACCGGGUUAAGAGGCCAGGCGUGCACGCAUAGCAAUGUGUUCAGCGGACUGGUGCUCAUCAGUCGAGGUCUUGACCACUC

实体 2 Entity 2 polymer

描述 description	50S ribosomal protein L3
分子量 formula_weight	22477.2 kDa
来源方法 src_method	nat
拷贝数 entity_count	1

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	B

MKGILGTKIGMTQIWKNDRAIPVTVVLAGPCPIVQRKTAQTDGYEAVQIGYAPKAERKVNKPMQGHFAKAGVAPTRILREFRGFAPDGDSVNVDIFAEGEKIDATGTSKGKGTQGVMKRWNFAGGPASHGSKKWHRRPGSIGQRKTPGRVYKGKRMAGHMGMERVTVQNLEVVEIRAGENLILVKGAIPGANGGLVVLRSAAKASAAKGGK

实体 3 Entity 3 non-polymer

描述 description	;(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 ;
分子量 formula_weight	477.7 kDa
来源方法 src_method	syn
拷贝数 entity_count	1

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7. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

结构域编号 domain_id	d2ognb1
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.43 — Reductase/isomerase/elongation factor common domain
超家族 Superfamily superfamily	b.43.3 — Translation proteins
家族 Family family	b.43.3.2 — Ribosomal protein L3

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8. 引用文献 (1)

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晶胞边长 a length_a	170.475 Å
晶胞边长 b length_b	412.738 Å
晶胞边长 c length_c	696.670 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	I 2 2 2
空间群编号 int_tables_number	23
晶系 crystal_system	—

分辨率 resolution	3.560 Å
最低分辨率 resolution_low	29.960 Å
R 因子 r_factor	—
R_work r_work	0.2760
R_free r_free	0.3380

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

The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080

1. 蛋白身份与相关结构 Protein Identity & Related Structures

50S ribosomal protein L3

当前结构中的状态

数据库中的同蛋白其他状态

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

2. 结构基本信息 2. Structure Basics

3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

5. 晶体学与实验 5. Crystallography & Experiment

晶胞参数 Unit Cell

对称性 Symmetry

精修参数 Refinement

6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

聚合物 Polymer

实体 2 Entity 2 polymer

聚合物 Polymer

实体 3 Entity 3 non-polymer

7. 折叠分类 (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

8. 引用文献 (1)

9. 文件与曲线 (10)

Files (7)

Curves (3)