5dk4

Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP

Method: X-RAY DIFFRACTION D_max: 78.5 Å Quality: GOOD

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

Tryptophan--tRNA ligase

Geobacillus stearothermophilus

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 2–328	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

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 5DK4	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
1I6K 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP Deposited 2001-03-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 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 × 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
1I6L 1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP Deposited 2001-03-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 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 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）	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 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）	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 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）	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 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）	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
7CKI Crystal structure of Tryptophanyl-tRNA synthetase from Bacillus stearothermophilus in complex with chuangxinmycin and ATP Deposited 2020-07-17	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）	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 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）	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 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_GEOSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–329； UniProt 2–328

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

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	5dk4
Deposition date deposition_date	2015-09-02
Structure title title	Crystal structure analysis of Tryptophanyl-trna synthetase from Bacillus stearothermophilus in complex with indolmycin and Mg*ATP
Keywords keywords	aaRS, inhibitor, LIGASE-LIGASE INHIBITOR complex; LIGASE/LIGASE INHIBITOR
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	21.81 Å
Radius of gyration Rg (electron density) rg_electron	20.85 Å
Forward intensity I(0) i0	26604000.00
Molecular weight molecular_weight	38417.0 kDa
Excluded volume excluded_volume	47559 Å³
Envelope volume envelope_volume	55465 Å³
Hydration-shell volume shell_volume	22372 Å³
Envelope diameter envelope_diameter	80.4 Å
Shell Rg shell_rg	27.39 Å
Envelope Rg envelope_rg	21.26 Å
Shape Rg shape_rg	20.86 Å
Total Rg total_rg	21.65 Å
Total atoms total_atoms	5328
Residues n_residues	318
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	78.5 Å
Rg (real space) rg_real	21.80 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.6600e+07
I(0) uncertainty (real space) i0_real_error	3.8020e+05
Rg (reciprocal space) rg_reciprocal	21.80 Å
I(0) (reciprocal space) i0_reciprocal	26600000.0000
Solution quality estimate total_estimate	0.8404
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.6 Å
Skewness Skewness skewness	0.397
Kurtosis Kurtosis kurtosis	-0.106
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6517000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.679; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.973

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tryptophan--tRNA ligase
Molecular weight formula_weight	37751.7 kDa
EC 编号 ec_number	6.1.1.2
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	5631

GMKTIFSGIQPSGVITIGNYIGALRQFVELQHEYNCYFCIVDQHAITVWQDPHELRQNIRRLAALYLAVGIDPTQATLFIQSEVPAHAQAAWMLQCIVYIGELERMTQFKEKSAGKEAVSAGLLTYPPLMAADILLYNTDIVPVGEDQKQHIELTRDLAERFNKRYGELFTIPEARIPKVGARIMSLVDPTKKMSKSDPNPKAYITLLDDAKTIEKKIKSAVTDSEGTIRYDKEAKPGISNLLNIYSTLSGQSIEELERQYEGKGYGVFKADLAQVVIETLRPIQERYHHWMESEELDRVLDEGAEKANRVASEMVRKMEQAMGLGRRR

来源 Source

来源生物 organism	Geobacillus stearothermophilus
NCBI Class编号 ncbi_taxonomy_id	1422
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	(5S)-5-[(1R)-1-(1H-indol-3-yl)ethyl]-2-(methylamino)-1,3-oxazol-4(5H)-one
Molecular weight formula_weight	257.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5dk4a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.26 — Adenine nucleotide alpha hydrolase-like
Superfamily Superfamily superfamily	c.26.1 — Nucleotidylyl transferase
Family Family family	c.26.1.1 — Class I aminoacyl-tRNA synthetases (RS), catalytic domain

Domain ID domain_id	d5dk4a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	5dk4A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	620 — HUPs

Domain ID domain_id	5dk4A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	240 — Tyrosyl-Transfer RNA Synthetase
Homologous superfamily homologous superfamily	10 — Tyrosyl-Transfer RNA Synthetase

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8. Citations (1)

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Unit-cell length a length_a	62.041 Å
Unit-cell length b length_b	62.041 Å
Unit-cell length c length_c	219.058 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	31.020 Å
R factor r_factor	0.1702
R_work r_work	0.1692
R_free r_free	0.1889

fit	/app/data/saxs_computation/dk/5dk4/5dk4.fit
pddf	/app/data/pr_computation/dk/5dk4/5dk4.pr.out
profile	/app/data/saxs_computation/dk/5dk4/5dk4.dat