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Yorodumi- PDB-7pqk: Co-Crystal Structure of M. tuberculosis LeuRS in Complex with the... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7pqk | |||||||||
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Title | Co-Crystal Structure of M. tuberculosis LeuRS in Complex with the Adduct Formed by Prodrug Cmpd1 with Adenosine-monophosphate | |||||||||
Components | Leucine--tRNA ligase | |||||||||
Keywords | LIGASE / Leucyl-tRNA Synthetase / catalyses the reaction: ATP + L-leucine + tRNA(Leu) = AMP + diphosphate + L-leucyl-tRNA(Leu) leucine-tRNA Ligase ATP binding domain | |||||||||
Function / homology | Function and homology information leucine-tRNA ligase / leucine-tRNA ligase activity / leucyl-tRNA aminoacylation / aminoacyl-tRNA editing activity / peptidoglycan-based cell wall / ATP binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å | |||||||||
Authors | Palencia, A. / Cusack, S. | |||||||||
Funding support | France, 2items
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Citation | Journal: J.Am.Chem.Soc. / Year: 2023 Title: Adenosine-Dependent Activation Mechanism of Prodrugs Targeting an Aminoacyl-tRNA Synthetase. Authors: Hoffmann, G. / Le Gorrec, M. / Mestdach, E. / Cusack, S. / Salmon, L. / Jensen, M.R. / Palencia, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7pqk.cif.gz | 135.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7pqk.ent.gz | 105 KB | Display | PDB format |
PDBx/mmJSON format | 7pqk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pq/7pqk ftp://data.pdbj.org/pub/pdb/validation_reports/pq/7pqk | HTTPS FTP |
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-Related structure data
Related structure data | 5agtS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24920.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Contain N-term His tag, Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: leuS, Rv0041, MTCY21D4.04 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WFV1, leucine-tRNA ligase |
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#2: Chemical | ChemComp-81D / ( |
#3: Chemical | ChemComp-EDO / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 42 % / Description: 3D-rods |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M Bis-TRIS (pH 5.5), 17% (w/v) PEG 10000 and 0.2 M ammonium acetate. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0615 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Silicon crystal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.0615 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.15→38.595 Å / Num. obs: 74820 / % possible obs: 98.4 % / Redundancy: 4.887 % / Biso Wilson estimate: 14.79 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.058 / Χ2: 0.948 / Net I/σ(I): 9.16 / Num. measured all: 476869 / Scaling rejects: 165 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5AGT Resolution: 1.15→38.595 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 18.46 / Stereochemistry target values: ML
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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 max: 56.7 Å2 / Biso mean: 23.43 Å2 / Biso min: 11.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.15→38.595 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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