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Open data
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Basic information
Entry | Database: PDB / ID: 7sew | ||||||
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Title | M. tb EgtD in complex with HD6 | ||||||
![]() | Histidine N-alpha-methyltransferase | ||||||
![]() | TRANSFERASE / Ergothioneine biosynthesis pathway / Rossmann fold domain / histidine/histamine derivatives / SAM dependent methyltransferase | ||||||
Function / homology | ![]() ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / dimethylhistidine N-methyltransferase activity / aminoacyl-tRNA ligase activity / protein methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sudasinghe, T.D. / Ronning, D.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Inhibitors of Mycobacterium tuberculosis EgtD target both substrate binding sites to limit hercynine production. Authors: Sudasinghe, T.D. / Banco, M.T. / Ronning, D.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 85.1 KB | Display | ![]() |
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PDB format | ![]() | 60.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 973 KB | Display | ![]() |
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Full document | ![]() | 975.1 KB | Display | |
Data in XML | ![]() | 17 KB | Display | |
Data in CIF | ![]() | 25 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7scfC ![]() 7sexC ![]() 7seyC ![]() 7sf4C ![]() 7sf5C ![]() 4uy5S 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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Unit cell |
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Components
#1: Protein | Mass: 35314.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: A0A045KE74, L-histidine Nalpha-methyltransferase | ||||||||
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#2: Chemical | #3: Chemical | ChemComp-A1I / | #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.61 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M sodium sulfate and 20 % w/v polyethylene glycol 1,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.72→49.35 Å / Num. obs: 31266 / % possible obs: 80.57 % / Redundancy: 1 % / CC1/2: 0.99 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.72→1.782 Å / Rmerge(I) obs: 0.35 / Num. unique obs: 1383 / CC1/2: 0.45 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4UY5 Resolution: 1.72→49.35 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.67 / 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: 66.79 Å2 / Biso mean: 24.304 Å2 / Biso min: 9.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.72→49.35 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
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