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Open data
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Basic information
Entry | Database: PDB / ID: 7sey | ||||||
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Title | M. tb EgtD in complex with SGH | ||||||
![]() | Histidine N-alpha-methyltransferase | ||||||
![]() | ![]() ![]() | ||||||
Function / homology | ![]() ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / ![]() ![]() 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 | ![]() | 135.9 KB | Display | ![]() |
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PDB format | ![]() | 104.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7scfC ![]() 7sewC ![]() 7sexC ![]() 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 | ChemComp-92W / |
#3: Water | ChemComp-HOH / ![]() |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 49.06 % |
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Crystal grow![]() | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M succinic acid pH 7.0 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![]() |
Reflection | Resolution: 2.39→46.31 Å / Num. obs: 12689 / % possible obs: 88.1 % / Redundancy: 16.9 % / Biso Wilson estimate: 50.82 Å2 / CC1/2: 0.99 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.39→2.476 Å / Rmerge(I) obs: 1.925 / Num. unique obs: 759 / CC1/2: 0.634 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 4UY5 Resolution: 2.39→46.31 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 36.29 / 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: 100.95 Å2 / Biso mean: 56.2407 Å2 / Biso min: 41.33 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.39→46.31 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16
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Refinement TLS params. | Method: refined / Origin x: -17.1914 Å / Origin y: 8.0421 Å / Origin z: 4.8614 Å
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Refinement TLS group |
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