+Open data
-Basic information
Entry | Database: PDB / ID: 7sex | ||||||
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Title | M. tb EgtD in complex with TGX221 | ||||||
Components | Histidine N-alpha-methyltransferase | ||||||
Keywords | TRANSFERASE / Ergothioneine biosynthesis pathway / Rossmann fold domain / histidine/histamine derivatives / SAM dependent methyltransferase | ||||||
Function / homology | Function and homology information ergothioneine biosynthetic process / L-histidine Nalpha-methyltransferase / : / aminoacyl-tRNA ligase activity / protein methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Sudasinghe, T.D. / Ronning, D.R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Rep / Year: 2021 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7sex.cif.gz | 142.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sex.ent.gz | 109 KB | Display | PDB format |
PDBx/mmJSON format | 7sex.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sex_validation.pdf.gz | 840.6 KB | Display | wwPDB validaton report |
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Full document | 7sex_full_validation.pdf.gz | 842 KB | Display | |
Data in XML | 7sex_validation.xml.gz | 14 KB | Display | |
Data in CIF | 7sex_validation.cif.gz | 18.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/se/7sex ftp://data.pdbj.org/pub/pdb/validation_reports/se/7sex | HTTPS FTP |
-Related structure data
Related structure data | 7scfC 7sewC 7seyC 7sf4C 7sf5C 4uy5S 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 on special symmetry positions |
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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.) Mycobacterium tuberculosis (bacteria) / Gene: egtD / Production host: Escherichia coli (E. coli) References: UniProt: A0A045KE74, L-histidine Nalpha-methyltransferase | ||||
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#2: Chemical | ChemComp-93I / | ||||
#3: Chemical | #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: 2.38 Å3/Da / Density % sol: 48.24 % |
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop Details: 0.2 M potassium phosphate dibasic and 20 % w/v polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.98 Å |
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: 2.2→49.31 Å / Num. obs: 17958 / % possible obs: 99.78 % / Redundancy: 1 % / Biso Wilson estimate: 38.47 Å2 / CC1/2: 0.95 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.201→2.279 Å / Num. unique obs: 1712 / CC1/2: 0.67 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UY5 Resolution: 2.2→49.31 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.4 / Phase error: 20.48 / 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: 103.35 Å2 / Biso mean: 42.9703 Å2 / Biso min: 23.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.2→49.31 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: -16.6702 Å / Origin y: 8.2787 Å / Origin z: 4.7753 Å
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Refinement TLS group |
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