[English] 日本語
Yorodumi- PDB-7daw: Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7daw | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Mycobacterium tuberculosis phenylalanyl-tRNA synthetase | ||||||
Components |
| ||||||
Keywords | LIGASE / aminoacylation / tRNA-binding / aminoacyl-tRNA synthetase / ATP-binding | ||||||
Function / homology | Function and homology information 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 | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å | ||||||
Authors | Xu, M. / Zhang, X. / Xu, L. / Chen, S. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2021 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: Journal: J.Biol.Chem. / Year: 2021 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7daw.cif.gz | 224.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7daw.ent.gz | 175.9 KB | Display | PDB format |
PDBx/mmJSON format | 7daw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/7daw ftp://data.pdbj.org/pub/pdb/validation_reports/da/7daw | HTTPS FTP |
---|
-Related structure data
Related structure data | 7db7C 7db8C 3pcoS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 37415.266 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pheS, Rv1649, MTCY06H11.14 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU3, phenylalanine-tRNA ligase | ||
---|---|---|---|
#2: Protein | Mass: 90179.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: pheT, Rv1650, MTCY06H11.15 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WFU1, phenylalanine-tRNA ligase | ||
#3: Chemical | ChemComp-SO4 / Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-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 |
---|
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97886 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97886 Å / Relative weight: 1 |
Reflection | Resolution: 2.83→50 Å / Num. obs: 59426 / % possible obs: 93.5 % / Redundancy: 2.7 % / Biso Wilson estimate: 59.32 Å2 / CC1/2: 0.964 / Rmerge(I) obs: 0.174 / Net I/σ(I): 10.86 |
Reflection shell | Resolution: 2.83→2.87 Å / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 2275 / CC1/2: 0.84 / % possible all: 71.5 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3PCO Resolution: 2.83→49.82 Å / SU ML: 0.3437 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.4372 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 61.02 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.83→49.82 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|