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Yorodumi- PDB-7noy: Crystal structure of the heterocyclic toxin methyltransferase fro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7noy | ||||||
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Title | Crystal structure of the heterocyclic toxin methyltransferase from Mycobacterium tuberculosis in complex with substrate 1-hydroxyquinolin-4(1H)-one | ||||||
Components | Uncharacterized protein Rv0560c | ||||||
Keywords | TRANSFERASE / Methyltransferase / HQNO-detoxification / SAM-dependent | ||||||
Function / homology | Function and homology information 2-heptyl-1-hydroxyquinolin-4(1H)-one methyltransferase / response to salicylic acid / cellular response to iron ion starvation / methyltransferase activity / methylation / response to hypoxia / cytosol Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Denkhaus, L. / Sartor, P. / Einsle, O. / Gerhardt, S. / Fetzner, S. | ||||||
Funding support | Germany, 1items
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Citation | Journal: J.Struct.Biol. / Year: 2021 Title: Structural basis of O-methylation of (2-heptyl-)1-hydroxyquinolin-4(1H)-one and related compounds by the heterocyclic toxin methyltransferase Rv0560c of Mycobacterium tuberculosis. Authors: Sartor, P. / Denkhaus, L. / Gerhardt, S. / Einsle, O. / Fetzner, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7noy.cif.gz | 106.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7noy.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 7noy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7noy_validation.pdf.gz | 502.8 KB | Display | wwPDB validaton report |
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Full document | 7noy_full_validation.pdf.gz | 502.8 KB | Display | |
Data in XML | 7noy_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | 7noy_validation.cif.gz | 10 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/no/7noy ftp://data.pdbj.org/pub/pdb/validation_reports/no/7noy | HTTPS FTP |
-Related structure data
Related structure data | 7bggSC 7ndmC 7nmkC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26420.482 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: Rv0560c / Plasmid: pET28b(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta pLysSRARE / References: UniProt: P9WKL5 | ||||
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#2: Chemical | ChemComp-SAH / | ||||
#3: Chemical | ChemComp-UK5 / | ||||
#4: Chemical | #5: 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: 2.55 Å3/Da / Density % sol: 51.78 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: Tacsimate pH 7 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.000043 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000043 Å / Relative weight: 1 |
Reflection | Resolution: 1.508→60.696 Å / Num. obs: 42031 / % possible obs: 98.1 % / Redundancy: 10.6 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.508→1.541 Å / Num. unique obs: 2104 / CC1/2: 0.742 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BGG Resolution: 1.8→51.16 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU R Cruickshank DPI: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.124 / SU Rfree Blow DPI: 0.117 / SU Rfree Cruickshank DPI: 0.109
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Displacement parameters | Biso mean: 20.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 1.8→51.16 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.81 Å / Total num. of bins used: 50
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Refinement TLS params. | Method: refined / Origin x: 24.1921 Å / Origin y: -19.5043 Å / Origin z: -12.8439 Å
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Refinement TLS group | Selection details: { A|* } |