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1i6k

1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP

Method: X-RAY DIFFRACTION Dmax: 77.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TRYPTOPHANYL-TRNA SYNTHETASE

OrganismNot specified

UniProt P00953

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–328 Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 14 NH4 AMMONIUM ION × 2 TYM TRYPTOPHANYL-5'AMP × 2 GOL GLYCEROL × 8 X-RAY DIFFRACTION X-ray crystallization conditions：MICRODIALYSIS；pH 7.6；310 K；POTASSIUM PHOSPHATE, AMMONIUM SULFATE, MAGNESIUM CHLORIDE, PEG 400, pH 7.60, MICRODIALYSIS, temperature 310K Resolution 1.72 Å R-free 0.268

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 1I6K Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1D2R 2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE. Deposited 1999-09-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–326（326 aa）
Chain D 1–326（326 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.8；315 K；2.0 M K2HPO4 , pH 6.8, MICRODIALYSIS, temperature 315K
Resolution 2.90 Å R-free 0.262
1D2R 2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE. Deposited 1999-09-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–326（326 aa）
Chain E 1–326（326 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.8；315 K；2.0 M K2HPO4 , pH 6.8, MICRODIALYSIS, temperature 315K
Resolution 2.90 Å R-free 0.262
1D2R 2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE. Deposited 1999-09-27 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–326（326 aa）
Chain F 1–326（326 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.8；315 K；2.0 M K2HPO4 , pH 6.8, MICRODIALYSIS, temperature 315K
Resolution 2.90 Å R-free 0.262
1I6L 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP Deposited 2001-03-02 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 14 NH4 AMMONIUM ION × 2 TYM TRYPTOPHANYL-5'AMP × 2 GOL GLYCEROL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.6；310 K；POTASSIUM PHOSPHATE, AMMONIUM SULFATE, MAGNESIUM SULFATE, pH 7.60, MICRODIALYSIS, temperature 310K
Resolution 1.72 Å R-free 0.241
1I6M 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP Deposited 2001-03-02 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Not recorded SO4 SULFATE ION × 14 NH4 AMMONIUM ION × 2 TYM TRYPTOPHANYL-5'AMP × 2 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.6；310 K；POTASSIUM PHOSPHATE, AMMONIUM SULFATE, MAGNESIUM SULFATE, pH 7.60, MICRODIALYSIS, temperature 310.0K
Resolution 1.72 Å R-free 0.257
1M83 Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in a Closed, Pre-transition State Conformation Deposited 2002-07-24 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；310 K；sodium citrate, sodium atp, magnesium chloride, pH 7.5, MICRODIALYSIS, temperature 310K
Resolution 2.20 Å R-free 0.252
1MAU Crystal structure of Tryptophanyl-tRNA Synthetase Complexed with ATP and Tryptophanamide in a Pre-Transition state Conformation Deposited 2002-08-02 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Not recorded NA SODIUM ION × 2 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LTN L-TRYPTOPHANAMIDE × 2 CIT CITRIC ACID × 2 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；310 K；sodium citrate, magnesium chloride, sodium ATP , l-tryptophanamide, pH 7.5, MICRODIALYSIS, temperature 310K
Resolution 2.15 Å R-free 0.243
1MAW Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in an Open Conformation Deposited 2002-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Chain D 1–328（328 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.6；310 K；potassium phosphate, mg-atp, pH 6.6, MICRODIALYSIS, temperature 310K
Resolution 3.00 Å R-free 0.253
1MAW Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in an Open Conformation Deposited 2002-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–328（328 aa）
Chain E 1–328（328 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.6；310 K；potassium phosphate, mg-atp, pH 6.6, MICRODIALYSIS, temperature 310K
Resolution 3.00 Å R-free 0.253
1MAW Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with ATP in an Open Conformation Deposited 2002-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–328（328 aa）
Chain F 1–328（328 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.6；310 K；potassium phosphate, mg-atp, pH 6.6, MICRODIALYSIS, temperature 310K
Resolution 3.00 Å R-free 0.253
1MB2 Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation Deposited 2002-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Chain D 1–328（328 aa）
Not recorded TRP TRYPTOPHAN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.6；310 K；potassium phosphate, l-tryptophan, pH 6.6, MICRODIALYSIS, temperature 310K
Resolution 2.70 Å R-free 0.254
1MB2 Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation Deposited 2002-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–328（328 aa）
Chain E 1–328（328 aa）
Not recorded TRP TRYPTOPHAN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.6；310 K；potassium phosphate, l-tryptophan, pH 6.6, MICRODIALYSIS, temperature 310K
Resolution 2.70 Å R-free 0.254
1MB2 Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Tryptophan in an Open Conformation Deposited 2002-08-02 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–328（328 aa）
Chain F 1–328（328 aa）
Not recorded TRP TRYPTOPHAN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 6.6；310 K；potassium phosphate, l-tryptophan, pH 6.6, MICRODIALYSIS, temperature 310K
Resolution 2.70 Å R-free 0.254
2OV4 Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in complex with adenosine tetraphosphate Deposited 2007-02-12 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Not recorded CS CESIUM ION × 2 AQP ADENOSINE-5'-TETRAPHOSPHATE × 2 ANL ANILINE × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions MICRODIALYSIS；pH 7.5；310 K；SODIUM CITRATE 1M, MAGRNESIUM ACETATE 10MM, ADENOSINE TETRAPHOSPHATE 10MM, PH 7.50, MICRODIALYSIS, temperature 310K
Resolution 2.50 Å R-free 0.258
3FHJ Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations Deposited 2008-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.28M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.65 Å R-free 0.270
3FHJ Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations Deposited 2008-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–328（328 aa）
Chain D 1–328（328 aa）
Not recorded TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.28M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.65 Å R-free 0.270
3FHJ Independent saturation of three TrpRS subsites generates a partially-assembled state similar to those observed in molecular simulations Deposited 2008-12-09 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 1–328（328 aa）
Chain F 1–328（328 aa）
Not recorded TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.28M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.65 Å R-free 0.270
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–326（326 aa）
Chain D 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–326（326 aa）
Chain E 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–326（326 aa）
Chain F 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain G 1–326（326 aa）
Chain J 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain H 1–326（326 aa）
Chain K 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain I 1–326（326 aa）
Chain L 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain M 1–326（326 aa）
Chain P 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain N 1–326（326 aa）
Chain Q 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
3FI0 Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate Deposited 2008-12-10 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain O 1–326（326 aa）
Chain R 1–326（326 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) TRP TRYPTOPHAN × 2 PO4 PHOSPHATE ION × 2 AMP ADENOSINE MONOPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.58；315 K；2.18 M K2HPO4, 0.6% (v/v) PEG 400, pH 6.58, dialysis, temperature 315K
Resolution 2.70 Å R-free 0.220
5DK4 Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP Deposited 2015-09-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–328（327 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ATP ADENOSINE-5'-TRIPHOSPHATE × 2 MG MAGNESIUM ION × 2 GOL GLYCEROL × 2 5BX (5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；298 K；hepes, potassium citrate, magnesium chloride
Resolution 1.90 Å R-free 0.189
7CKI Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin and ATP Deposited 2020-07-17 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Not recorded 9E0 (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid × 2 MG MAGNESIUM ION × 2 K POTASSIUM ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；310 K；1.8 M K2HPO4
Resolution 2.30 Å R-free 0.208
7CMS Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin Deposited 2020-07-28 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Chain B 1–328（328 aa）
Not recorded 9E0 (5~{S},6~{R})-5-methyl-7-thia-2-azatricyclo[6.3.1.0^{4,12}]dodeca-1(12),3,8,10-tetraene-6-carboxylic acid × 2 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；310 K；1.8M K2HPO4
Resolution 2.20 Å R-free 0.209
7EER Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with 05E6 and ATP Deposited 2021-03-19 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–328（328 aa）
Mutation：K64L ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZCW 2-(1H-indol-3-yl)ethanol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；310 K；1.9 M K2HPO4
Resolution 2.00 Å R-free 0.255
7EER Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with 05E6 and ATP Deposited 2021-03-19 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 1–328（328 aa）
Mutation：K64L ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZCW 2-(1H-indol-3-yl)ethanol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；310 K；1.9 M K2HPO4
Resolution 2.00 Å R-free 0.255
7EER Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with 05E6 and ATP Deposited 2021-03-19 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 1–328（328 aa）
Chain D 1–328（328 aa）
Mutation：K64L Mutation：K64L ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ZCW 2-(1H-indol-3-yl)ethanol × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；310 K；1.9 M K2HPO4
Resolution 2.00 Å R-free 0.255

14 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SYW_BACST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–328； UniProt 1–328

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

SAXS profile for 1i6k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1i6k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1i6k
Deposition date deposition_date2001-03-02
Structure title title1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP
Keywords keywordsCLASS I TRNA SYNTHETASE, AARS, INDUCED FIT, TRPRS, LIGASE; LIGASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.84 Å
Radius of gyration Rg (electron density) rg_electron20.71 Å
Forward intensity I(0) i027873400.00
Molecular weight molecular_weight38912.0 kDa
Excluded volume excluded_volume47890 ų
Envelope volume envelope_volume54866 ų
Hydration-shell volume shell_volume22226 ų
Envelope diameter envelope_diameter79.2 Å
Shell Rg shell_rg27.42 Å
Envelope Rg envelope_rg21.05 Å
Shape Rg shape_rg20.69 Å
Total Rg total_rg21.56 Å
Total atoms total_atoms2687
Residues n_residues316
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax77.2 Å
Rg (real space) rg_real21.80 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real2.7870e+07
I(0) uncertainty (real space) i0_real_error4.4550e+05
Rg (reciprocal space) rg_reciprocal21.81 Å
I(0) (reciprocal space) i0_reciprocal27870000.0000
Solution quality estimate total_estimate0.8553
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2 Å
Skewness Skewness skewness0.336
Kurtosis Kurtosis kurtosis-0.237
Angular range angular_range— – 0.3650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5959000.0000
Real-space data points n_real_points68
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.731; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.980
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1i6ka_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamilyc.26.1 — Nucleotidylyl transferase
Family Family familyc.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id1i6kA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily620 — HUPs
Domain ID domain_id1i6kA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily10 — Tyrosyl-Transfer RNA Synthetase
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8. Citations (1)

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9. Files and Curves (10)