1d2r

2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.

Method: X-RAY DIFFRACTION D_max: 180.1 Å Quality: GOOD

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

PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–326 Chain D； UniProt 1–326	Not recorded	No other associated polymer	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–326 Chain E； UniProt 1–326	Not recorded	No other associated polymer	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
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–326 Chain F； UniProt 1–326	Not recorded	No other associated polymer	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

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 1D2R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I6K 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）	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 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）	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 30 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 1–326； UniProt 1–326 Author chain B； PDBConstruct 1–326； UniProt 1–326 Author chain C； PDBConstruct 1–326； UniProt 1–326 Author chain D； PDBConstruct 1–326； UniProt 1–326 Author chain E； PDBConstruct 1–326； UniProt 1–326 Author chain F； PDBConstruct 1–326； UniProt 1–326

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	1d2r
Deposition date deposition_date	1999-09-27
Structure title title	2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.
Keywords keywords	CLASS I TRNA SYNTHETASE, AARS, INDUCED FIT, TRPRS, LIGASE; LIGASE
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	50.66 Å
Radius of gyration Rg (electron density) rg_electron	50.72 Å
Forward intensity I(0) i0	692083000.00
Molecular weight molecular_weight	220200.0 kDa
Excluded volume excluded_volume	276660 Å³
Envelope volume envelope_volume	390540 Å³
Hydration-shell volume shell_volume	66668 Å³
Envelope diameter envelope_diameter	190.6 Å
Shell Rg shell_rg	51.53 Å
Envelope Rg envelope_rg	49.92 Å
Shape Rg shape_rg	50.72 Å
Total Rg total_rg	50.74 Å
Total atoms total_atoms	15480
Residues n_residues	1956
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	180.1 Å
Rg (real space) rg_real	50.72 Å
Rg uncertainty (real space) rg_real_error	2.12 Å
I(0) (real space) i0_real	6.9210e+08
I(0) uncertainty (real space) i0_real_error	1.2650e+07
Rg (reciprocal space) rg_reciprocal	50.61 Å
I(0) (reciprocal space) i0_reciprocal	692000000.0000
Solution quality estimate total_estimate	0.8604
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	69.7 Å
Skewness Skewness skewness	0.309
Kurtosis Kurtosis kurtosis	-0.289
Angular range angular_range	— – 0.1550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48820000.0000
Real-space data points n_real_points	32
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.926; Smooth: 0.869

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1d2ra_
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	d1d2rb_
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	d1d2rc_
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	d1d2rd_
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	d1d2re_
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	d1d2rf_
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

CATH v4.4 (12 domains)

Domain ID domain_id	1d2rA01
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	1d2rA02
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

Domain ID domain_id	1d2rB01
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	1d2rB02
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

Domain ID domain_id	1d2rC01
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	1d2rC02
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

Domain ID domain_id	1d2rD01
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	1d2rD02
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

Domain ID domain_id	1d2rE01
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	1d2rE02
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

Domain ID domain_id	1d2rF01
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	1d2rF02
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	226.760 Å
Unit-cell length b length_b	91.660 Å
Unit-cell length c length_c	156.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	132.66 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2370
R_work r_work	0.2370
R_free r_free	0.2620

Description description	PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)
Molecular weight formula_weight	36751.1 kDa
EC 编号 ec_number	6.1.1.2
Source method src_method	nat
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	15480

2.9 A CRYSTAL STRUCTURE OF LIGAND-FREE TRYPTOPHANYL-TRNA SYNTHETASE: DOMAIN MOVEMENTS FRAGMENT THE ADENINE NUCLEOTIDE BINDING SITE.

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

PROTEIN (TRYPTOPHANYL TRNA SYNTHETASE)

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (6 domains)

CATH v4.4 (12 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/d2/1d2r/1d2r.fit
pddf	/app/data/pr_computation/d2/1d2r/1d2r.pr.out
profile	/app/data/saxs_computation/d2/1d2r/1d2r.dat