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- PDB-7el8: Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7el8 | ||||||
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Title | Crystal structure of Mycobacterium tuberculosis tryptophanyl-tRNA synthetase | ||||||
![]() | Tryptophan--tRNA ligase | ||||||
![]() | LIGASE / 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. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.8 KB | Display | ![]() |
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PDB format | ![]() | 57.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 422.9 KB | Display | ![]() |
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Full document | ![]() | 427.4 KB | Display | |
Data in XML | ![]() | 15.1 KB | Display | |
Data in CIF | ![]() | 21.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7eltC ![]() 7ensC ![]() 7entC ![]() 7ev2C ![]() 7ev3C ![]() 5dk4S 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.) ![]() ![]() ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.32 % |
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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 6M / Detector: PIXEL / Date: Jan 4, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97853 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→50 Å / Num. obs: 23425 / % possible obs: 100 % / Redundancy: 36.6 % / Biso Wilson estimate: 25.46 Å2 / CC1/2: 0.912 / CC star: 0.977 / Rmerge(I) obs: 0.129 / Net I/σ(I): 5 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 38.3 % / Rmerge(I) obs: 0.964 / Mean I/σ(I) obs: 6.75 / Num. unique obs: 1133 / CC1/2: 0.975 / CC star: 0.994 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5DK4 Resolution: 2.1→48.16 Å / SU ML: 0.2114 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.7527 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: 32.15 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→48.16 Å
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Refine LS restraints |
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LS refinement shell |
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