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CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS

Method: X-RAY DIFFRACTION D_max: 79.7 Å Quality: REASONABLE

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

50S ribosomal protein L1

Thermus thermophilus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein–RNA Monomer Protein × 1 RNA 1 PDB declaration: dimeric（2） Consistent with all polymer counts	Chain A； UniProt 10–229	Not recorded	23S ribosomal RNA × 1 MLI MALONATE ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；2.4 M sodium malonate	Resolution 2.70 Å R-free 0.249

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 5NPM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AD2 RIBOSOMAL PROTEIN L1 MUTANT WITH SERINE 179 REPLACED BY CYSTEINE Deposited 1997-02-20	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 1–228（228 aa）	Mutation：S179C	SO4 SULFATE ION × 3 HG MERCURY (II) ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions DROPS CONTAINING: APPR. 15 MG/ML L1 50 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL	Resolution 1.90 Å R-free 0.270
1EG0 FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME Deposited 2000-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 11 PDB declaration: pentadecameric	Chain N 1–229（229 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM cryo-EM vitrification conditions Cryogen ETHANE	Resolution 11.50 Å
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain E 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
1ZHO The structure of a ribosomal protein L1 in complex with mRNA Deposited 2005-04-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain G 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	K POTASSIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；KCl, MgCl2, HgCl2, PEG 10000, cacodylate, glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.60 Å R-free 0.281
2HW8 Structure of ribosomal protein L1-mRNA complex at 2.1 resolution. Deposited 2006-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–228（228 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1 K POTASSIUM ION × 1 BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG1000, sodium cacodylate,0.5% glycerol, 0.2 mM HgCl2 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.247
2OUM The first domain of L1 from Thermus thermophilus Deposited 2007-02-12	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 2–68（67 aa） Chain A 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM acetate Na, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.55 Å R-free 0.270
2OV7 The first domain of the ribosomal protein L1 from Thermus thermophilus Deposited 2007-02-13	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 2–68（67 aa） Chain A 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.233
2OV7 The first domain of the ribosomal protein L1 from Thermus thermophilus Deposited 2007-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–68（67 aa） Chain B 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.233
2OV7 The first domain of the ribosomal protein L1 from Thermus thermophilus Deposited 2007-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 2–68（67 aa） Chain C 160–229（70 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；277 K；30% v/v polyethylenglycol 4K, 100 mM Tris-HCl, 200 mM LiSO4, pH 8.5, VAPOR DIFFUSION, temperature 277K	Resolution 2.30 Å R-free 0.233
2VPL The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii Deposited 2008-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 2–68（67 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229 Chain A 160–229（70 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.274
2VPL The structure of the complex between the first domain of L1 protein from Thermus thermophilus and mRNA from Methanococcus jannaschii Deposited 2008-03-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain C 2–68（67 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229 Chain C 160–229（70 aa） Fragment：FIRST DOMAIN, RESIDUES 2-68,160-229	Not recorded	K POTASSIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å R-free 0.274
3TG8 Mutant ribosomal protein L1 lacking ala158 from thermus thermophilus Deposited 2011-08-17	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 1–229（229 aa）	Mutation：lacking A158	PG4 TETRAETHYLENE GLYCOL × 3 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；30 mM Tris-HCl, 75 mM NaCl with of 15% PEG 4K, 50 mM Tris-HCl, 0.2 M KBr (# 10 of Clear Strategy Screen I (MDL)) and 14% 2-methyl-2,4-pentandiol, 0.25 M MgCl2 in a 4:1:1, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 7.5	Resolution 1.95 Å R-free 0.226
3U4M Crystal structure of ribosomal protein tthl1 in complex with 80nt 23s rna from thermus thermophilus Deposited 2011-10-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–229（229 aa）	Mutation：V218R	SO4 SULFATE ION × 2 MLI MALONATE ION × 7 MG MAGNESIUM ION × 5 CL CHLORIDE ION × 2 NA SODIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；50mM NaCl, 2.5M Ammonium sulfate, 50mM MES, 10mM Magnesium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.208
3U56 Crystal structure of mutant ribosomal protein T217V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2011-10-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–229（229 aa）	Mutation：V218R	MG MAGNESIUM ION × 11 MLI MALONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；295 K；50mM NaCl, 2.5M Ammonium sulfate, 50mM MES, 10mM Magnesium acetate , pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.10 Å R-free 0.238
3UMY Crystal structure of mutant ribosomal protein T217A TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2011-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 2–229（228 aa）	Mutation：T217A	CL CHLORIDE ION × 2 SO4 SULFATE ION × 5 NA SODIUM ION × 1 MG MAGNESIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；295 K；2.0 M Ammonium sulfate, 0.1 M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.90 Å R-free 0.246
487D SEVEN RIBOSOMAL PROTEINS FITTED TO A CRYO-ELECTRON MICROSCOPIC MAP OF THE LARGE 50S SUBUNIT AT 7.5 ANGSTROMS RESOLUTION Deposited 2000-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 6–229（224 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions	Resolution 7.50 Å
4F9T Ribosomal protein L1 from Thermus thermophilus with substitution Thr217Ala Deposited 2012-05-21	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 1–229（229 aa）	Mutation：T217A	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；295 K；15 MG/ML L1 50 MM GLYCINE,INITIALLY AT PH 10 5% (V/V)METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL , VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.46 Å R-free 0.202
4QG3 Crystal structure of mutant ribosomal protein G219V TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2014-05-22	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 2–229（228 aa）	Mutation：G219V	SO4 SULFATE ION × 5 IPA ISOPROPYL ALCOHOL × 8 BME BETA-MERCAPTOETHANOL × 4 URE UREA × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；1.8 M Ammonium sulfate, 0.05 M Bis-Tris,pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.226
4QGB Crystal structure of mutant ribosomal protein G219V TthL1 Deposited 2014-05-22	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 14–229（216 aa）	Mutation：G219V	CL CHLORIDE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2 M ammonium sulfate, 0.1 M sodium acetate, 0.5 l 0.65% polyacrylic acid 5100 sodium salt, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.251
4QGB Crystal structure of mutant ribosomal protein G219V TthL1 Deposited 2014-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 14–229（216 aa）	Mutation：G219V	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2 M ammonium sulfate, 0.1 M sodium acetate, 0.5 l 0.65% polyacrylic acid 5100 sodium salt, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.251
4QGB Crystal structure of mutant ribosomal protein G219V TthL1 Deposited 2014-05-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 14–229（216 aa） Chain B 14–229（216 aa）	Mutation：G219V Mutation：G219V	CL CHLORIDE ION × 3 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；2 M ammonium sulfate, 0.1 M sodium acetate, 0.5 l 0.65% polyacrylic acid 5100 sodium salt, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.251
4QVI Crystal structure of mutant ribosomal protein M218L TthL1 in complex with 80nt 23S RNA from Thermus thermophilus Deposited 2014-07-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–229（229 aa）	Mutation：M218L	SO4 SULFATE ION × 4 ACT ACETATE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；2.5 M ammonium sulfate, 0.05M MES , 0.01M Magnesium Acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.217
4REO Mutant ribosomal protein l1 from thermus thermophilus with threonine 217 replaced by valine Deposited 2014-09-23	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 1–229（229 aa）	Mutation：T217V	SO4 SULFATE ION × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 GLY GLYCINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 10；295 K；15 MG/ML L1 50 MM GLYCINE, INITIALLY AT PH 10 5% (V/V) METHANE PENTANEDIOL 1.2 M AMMONIUM SULFATE EQUILIBRATED AGAINST 2.4 M AMMONIUM SULFATE 7% (V/V) METHANE PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 1.35 Å R-free 0.209
4V42 Crystal structure of the ribosome at 5.5 A resolution. Deposited 2001-03-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 42 PDB declaration: 49-meric	Chain BC 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 5.50 Å
4V4P Crystal structure of 70S ribosome with thrS operator and tRNAs. Deposited 2005-01-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 58-meric	Chain AC 1–228（228 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.50 Å R-free 0.356
4V4X Crystal structure of the 70S Thermus thermophilus ribosome showing how the 16S 3'-end mimicks mRNA E and P codons. Deposited 2006-06-27	Different construct 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 BC 0–228（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.00 Å R-free 0.323
4V4Y Crystal structure of the 70S Thermus thermophilus ribosome with translocated and rotated Shine-Dalgarno Duplex. Deposited 2006-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric	Chain BC 0–228（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.50 Å R-free 0.326
4V4Z 70S Thermus thermophilous ribosome functional complex with mRNA and E- and P-site tRNAs at 4.5A. Deposited 2006-06-27	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 56-meric	Chain BC 0–228（229 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 4.51 Å R-free 0.345
4WU1 Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-site Deposited 2014-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 54-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 708 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.20 Å R-free 0.238
4WU1 Complex of 70S ribosome with tRNA-Tyr and mRNA with G-U mismatch in the second position in the P-site Deposited 2014-10-30	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 48 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 673 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.20 Å R-free 0.238
4WZD Complex of 70S ribosome with cognate tRNA-Tyr in the P-site Deposited 2014-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 699 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.10 Å R-free 0.193
4WZD Complex of 70S ribosome with cognate tRNA-Tyr in the P-site Deposited 2014-11-19	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 55-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 646 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.10 Å R-free 0.193
4WZO Complex of 70S ribosome with tRNA-fMet and mRNA Deposited 2014-11-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 56-MERIC	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 576 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；Tris-acetate, KSCN, PEG 550MME, PEG 20K	Resolution 3.30 Å R-free 0.258
5E7K Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site Deposited 2015-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 628 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.20 Å R-free 0.258
5E7K Structure of T. thermophilus 70S ribosome complex with mRNA and cognate tRNALys in the A-site Deposited 2015-10-12	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 510 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.20 Å R-free 0.258
5EL5 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-MERIC	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 660 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.15 Å R-free 0.254
5EL6 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 593 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.10 Å R-free 0.249
5EL6 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the first position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 480 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.10 Å R-free 0.249
5EL7 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 687 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.15 Å R-free 0.247
5EL7 Structure of T. thermophilus 70S ribosome complex with mRNA and tRNALys in the A-site with a U-U mismatch in the second position and antibiotic paromomycin Deposited 2015-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 574 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.15 Å R-free 0.247
5IB7 Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet, near-cognate tRNALys with U-G mismatch in the A-site and antibiotic paromomycin Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 56-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 695 PAR PAROMOMYCIN × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 2.99 Å R-free 0.241
5IB8 Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and near-cognate tRNALys with U-G mismatch in the A-site Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 723 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 3.13 Å R-free 0.244
5IBB Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 736 SPE THERMINE × 1 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 2.96 Å R-free 0.243
5IBB Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAVal in the A-site Deposited 2016-02-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 48 PDB declaration: 55-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 608 SPE THERMINE × 4 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；PEG 20000, PEG 550mme, KSCN, Tris-OAc	Resolution 2.96 Å R-free 0.243
5IMQ Structure of ribosome bound to cofactor at 3.8 angstrom resolution Deposited 2016-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric	Chain Z 1–229（229 aa）	Not recorded	GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer G 5 mM HEPES pH 7.5, 10 mM MgAc, 50 mM KCl, 10 mM NH4Cl, and 6 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5IMR Structure of ribosome bound to cofactor at 5.7 angstrom resolution Deposited 2016-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 56-meric	Chain Z 1–229（229 aa）	Not recorded	GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；Buffer G 5 mM HEPES pH 7.5, 10 mM MgAc, 50 mM KCl, 10 mM NH4Cl, and 6 mM 2-mercaptoethanol cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.70 Å
5J8B Crystal structure of Elongation Factor 4 (EF-4/LepA) in complex with GDPCP bound to the Thermus thermophilus 70S ribosome Deposited 2016-04-07	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 52 PDB declaration: 59-meric	Chain C 2–229（228 aa）	Not recorded	MG MAGNESIUM ION × 919 ZN ZINC ION × 6 SF4 IRON/SULFUR CLUSTER × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.6；292 K；0.1-0.2 M Arginine-HCl, 0.1M Tris-HCl pH 7.6, 2.6-3.0% PEG-20K, 7-10% MPD, 0.5mM BME	Resolution 2.60 Å R-free 0.261
5ZLU Ribosome Structure bound to ABC-F protein. Deposited 2018-03-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 57-meric	Chain Y 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GSL Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAArg in the A-site Deposited 2018-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 60-meric	Chain 71 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 954 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Tris-OAc, KSCN, PEG-20000, PEG-550mme	Resolution 3.16 Å
6GSL Structure of T. thermophilus 70S ribosome complex with mRNA, tRNAfMet and cognate tRNAArg in the A-site Deposited 2018-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 47 PDB declaration: 54-meric	Chain 79 1–229（229 aa）	Not recorded	MG MAGNESIUM ION × 810 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Tris-OAc, KSCN, PEG-20000, PEG-550mme	Resolution 3.16 Å
6QNQ 70S ribosome initiation complex (IC) with experimentally assigned potassium ions Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric	Chain 71 1–229（229 aa）	Not recorded	K POTASSIUM ION × 169 MG MAGNESIUM ION × 543 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；Tris-OAc, KSCN, PEG-20K, PEG-550mme	Resolution 3.50 Å R-free 0.251
6QNR 70S ribosome elongation complex (EC) with experimentally assigned potassium ions Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 57-meric	Chain 71 1–229（229 aa）	Not recorded	K POTASSIUM ION × 211 MG MAGNESIUM ION × 585 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Tris-OAc, KSCN, PEG-20k, PEG-550mme	Resolution 3.10 Å R-free 0.253
6QNR 70S ribosome elongation complex (EC) with experimentally assigned potassium ions Deposited 2019-02-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–RNA Heteromer；Protein × 49 PDB declaration: 56-meric	Chain 79 1–229（229 aa）	Not recorded	K POTASSIUM ION × 155 MG MAGNESIUM ION × 409 SF4 IRON/SULFUR CLUSTER × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Tris-OAc, KSCN, PEG-20k, PEG-550mme	Resolution 3.10 Å R-free 0.253

39 other PDB entries and 55 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RL1_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–220； UniProt 10–229

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5npm
Deposition date deposition_date	2017-04-17
Structure title title	CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS
Keywords keywords	ribosome, 50S, 23S rRNA, L1 stalk, RNA; RNA
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	23.52 Å
Radius of gyration Rg (electron density) rg_electron	23.39 Å
Forward intensity I(0) i0	75654000.00
Molecular weight molecular_weight	48936.0 kDa
Excluded volume excluded_volume	53027 Å³
Envelope volume envelope_volume	71284 Å³
Hydration-shell volume shell_volume	25937 Å³
Envelope diameter envelope_diameter	81.7 Å
Shell Rg shell_rg	30.03 Å
Envelope Rg envelope_rg	23.17 Å
Shape Rg shape_rg	23.36 Å
Total Rg total_rg	24.02 Å
Total atoms total_atoms	3331
Residues n_residues	291
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	79.7 Å
Rg (real space) rg_real	23.47 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	7.5650e+07
I(0) uncertainty (real space) i0_real_error	9.1080e+05
Rg (reciprocal space) rg_reciprocal	23.48 Å
I(0) (reciprocal space) i0_reciprocal	75650000.0000
Solution quality estimate total_estimate	0.6680
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.318
Kurtosis Kurtosis kurtosis	-0.196
Angular range angular_range	— – 0.3400 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	5029000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.780; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.997; Smooth: 0.998

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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	50S ribosomal protein L1
Molecular weight formula_weight	23708.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3340

ALLEKVDPNKIYTIDEAAHLVKELATAKFDETVEVHAKLGIDPRRSDQNVRGTVSLPHGLGKQVRVLAIAKGEKIKEAEEAGADYVGGEEIIQKILDGWMDFDAVVATPDVMGAVGSKLGRILGPRGLLPNPKAGTVGFNIGEIIREIKAGRIEFRNDKTGAIHAPVGKASFPPEKLADNIRAFIRALEAHKPEGAKGTFLRSVYVTTTMGPSVRINPHS

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	23S ribosomal RNA
Molecular weight formula_weight	25974.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	B

GGGAUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUUCCC

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5npmA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	190 — Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase
Homologous superfamily homologous superfamily	20 — Ribosomal protein L1/L10, rRNA-binding domain

Domain ID domain_id	5npmA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	790 — Ribosomal protein L1/L10, domain II

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8. Citations (1)

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Unit-cell length a length_a	64.127 Å
Unit-cell length b length_b	65.532 Å
Unit-cell length c length_c	119.925 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	25.341 Å
R factor r_factor	0.2042
R_work r_work	0.2018
R_free r_free	0.2486

fit	/app/data/saxs_computation/np/5npm/5npm.fit
pddf	/app/data/pr_computation/np/5npm/5npm.pr.out
profile	/app/data/saxs_computation/np/5npm/5npm.dat

CRYSTAL STRUCTURE OF MUTANT RIBOSOMAL PROTEIN TTHL1 LACKING 8 N-TERMINAL RESIDUES IN COMPLEX WITH 80NT 23S RNA FROM THERMUS THERMOPHILUS

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

50S ribosomal protein L1

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

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)