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- PDB-7ev3: Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7ev3 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase complexed with Y-10 and ATP | ||||||
![]() | Tryptophan--tRNA ligase | ||||||
![]() | LIGASE / TrpRS / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding | ||||||
Function / homology | ![]() tryptophan-tRNA ligase / tryptophan-tRNA ligase activity / tryptophanyl-tRNA aminoacylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, M. / Chen, S. | ||||||
![]() | ![]() Title: Investigate Natural Product Indolmycin and the Synthetically Improved Analogue Toward Antimycobacterial Agents. Authors: Yang, Y. / Xu, Y. / Yue, Y. / Wang, H. / Cui, Y. / Pan, M. / Zhang, X. / Zhang, L. / Li, H. / Xu, M. / Tang, Y. / Chen, S. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 81 KB | Display | ![]() |
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PDB format | ![]() | 56.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 14.3 KB | Display | |
Data in CIF | ![]() | 19.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7el8SC ![]() 7eltC ![]() 7ensC ![]() 7entC ![]() 7ev2C S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 37380.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: trpS, DSI38_02915, E5M05_20150, E5M52_19725, E5M78_19780, ERS007657_01660, ERS007661_00440, ERS007663_02313, ERS007665_01484, ERS007670_03000, ERS007679_02115, ERS007681_00969, ERS007688_01638, ...Gene: trpS, DSI38_02915, E5M05_20150, E5M52_19725, E5M78_19780, ERS007657_01660, ERS007661_00440, ERS007663_02313, ERS007665_01484, ERS007670_03000, ERS007679_02115, ERS007681_00969, ERS007688_01638, ERS007703_02455, ERS007722_03290, ERS007741_01346, ERS013471_03442, ERS023446_03614, ERS024276_00235, ERS027659_00823, ERS094182_03915, F6W99_01991, GCL30_20825, SAMEA2683035_03669 Production host: ![]() ![]() |
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#2: Chemical | ChemComp-ATP / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-JE3 / ( |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.42 Å3/Da / Density % sol: 49.12 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.7 / Details: 0.2M MgCl2, 35% PEG 400, 0.1M MES, pH 5.7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→50 Å / Num. obs: 11213 / % possible obs: 99.8 % / Redundancy: 21.8 % / Biso Wilson estimate: 44.17 Å2 / CC1/2: 0.978 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.7→2.75 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 530 / CC1/2: 0.865 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7EL8 Resolution: 2.7→47.89 Å / SU ML: 0.3056 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.6382 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.36 Å2 | |||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→47.89 Å
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Refine LS restraints |
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LS refinement shell |
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