+Open data
-Basic information
Entry | Database: PDB / ID: 7sf5 | ||||||
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Title | M. tb EgtD in complex with HD3 | ||||||
Components | Histidine N-alpha-methyltransferase | ||||||
Keywords | TRANSFERASE / SAM dependent methyl transferase / peptide like inhibitor / SAM binding domain / Histidine binding domain | ||||||
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: 2.52 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 | 7sf5.cif.gz | 137.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7sf5.ent.gz | 105.9 KB | Display | PDB format |
PDBx/mmJSON format | 7sf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7sf5_validation.pdf.gz | 970.8 KB | Display | wwPDB validaton report |
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Full document | 7sf5_full_validation.pdf.gz | 976.2 KB | Display | |
Data in XML | 7sf5_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 7sf5_validation.cif.gz | 33.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sf/7sf5 ftp://data.pdbj.org/pub/pdb/validation_reports/sf/7sf5 | HTTPS FTP |
-Related structure data
Related structure data | 7scfC 7sewC 7sexC 7seyC 7sf4C 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 1 - 321 / Label seq-ID: 1 - 321
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-Components
#1: Protein | Mass: 35314.789 Da / Num. of mol.: 2 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 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.3 % |
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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: Aug 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: 2.52→50.27 Å / Num. obs: 24381 / % possible obs: 99.86 % / Redundancy: 1 % / CC1/2: 0.98 / Net I/σ(I): 11 |
Reflection shell | Resolution: 2.52→2.61 Å / Num. unique obs: 2384 / CC1/2: 0.55 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4UY5 Resolution: 2.52→50.27 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.37 / 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: 86.43 Å2 / Biso mean: 35.6355 Å2 / Biso min: 10.75 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.52→50.27 Å
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Refine LS restraints NCS |
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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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