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- PDB-7db7: Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7db7 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase in complex with compound GDI05-001 | ||||||
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![]() | LIGASE / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding | ||||||
Function / homology | ![]() phenylalanine-tRNA ligase complex / phenylalanine-tRNA ligase / phenylalanine-tRNA ligase activity / phenylalanyl-tRNA aminoacylation / peptidoglycan-based cell wall / tRNA binding / magnesium ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Xu, M. / Zhang, X. / Xu, L. / Chen, S. | ||||||
![]() | ![]() Title: Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis . Authors: Wang, H. / Xu, M. / Engelhart, C.A. / Zhang, X. / Yan, B. / Pan, M. / Xu, Y. / Fan, S. / Liu, R. / Xu, L. / Hua, L. / Schnappinger, D. / Chen, S. #1: ![]() Title: Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis Authors: Wang, H. / Xu, M. / Engelhart, C.A. / Zhang, X. / Yan, B. / Pan, M. / Xu, Y. / Fan, S. / Liu, R. / Xu, L. / Hua, L. / Schnappinger, D. / Chen, S. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 233.3 KB | Display | ![]() |
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PDB format | ![]() | 181 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 791.4 KB | Display | ![]() |
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Full document | ![]() | 797.3 KB | Display | |
Data in XML | ![]() | 39.9 KB | Display | |
Data in CIF | ![]() | 57.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7dawSC ![]() 7db8C 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
#1: Protein | Mass: 37415.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: pheS, Rv1649, MTCY06H11.14 / Production host: ![]() ![]() | ||||
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#2: Protein | Mass: 90179.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 25618 / H37Rv / Gene: pheT, Rv1650, MTCY06H11.15 / Production host: ![]() ![]() | ||||
#3: Chemical | ChemComp-H2L / | ||||
#4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 1.1M (NH4)2SO4, 0.2% PEG 3350, 0.1M HEPES pH 7.5 |
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-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 7, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97849 Å / Relative weight: 1 |
Reflection | Resolution: 2.71→50 Å / Num. obs: 72740 / % possible obs: 99.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 45.3 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.133 / Net I/σ(I): 10.42 |
Reflection shell | Resolution: 2.71→2.75 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 3.26 / Num. unique obs: 3594 / CC1/2: 0.851 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7DAW Resolution: 2.71→42.16 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.1371 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: 43.54 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.71→42.16 Å
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Refine LS restraints |
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LS refinement shell |
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