+
Open data
-
Basic information
Entry | Database: PDB / ID: 7scf | ||||||
---|---|---|---|---|---|---|---|
Title | M. tb EgtD in complex with HD2 | ||||||
![]() | 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 | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 253.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 204 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 25.4 KB | Display | |
Data in CIF | ![]() | 34.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7sewC ![]() 7sexC ![]() 7seyC ![]() 7sf4C ![]() 7sf5C ![]() 4uy5S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 35314.789 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: egtD, C0094_20235, DSI38_25660, E5M05_18135, E5M52_16355, E5M78_15990, ERS007657_01802, ERS007663_00740, ERS007665_01629, ERS007670_03296, ERS007741_03430, ERS013471_00673, ERS024276_01805, ...Gene: egtD, C0094_20235, DSI38_25660, E5M05_18135, E5M52_16355, E5M78_15990, ERS007657_01802, ERS007663_00740, ERS007665_01629, ERS007670_03296, ERS007741_03430, ERS013471_00673, ERS024276_01805, ERS094182_02516, F6W99_02380, GCL30_14140, SAMEA2683035_00801 Production host: ![]() ![]() References: UniProt: A0A045KE74, L-histidine Nalpha-methyltransferase |
---|
-Non-polymers , 5 types, 105 molecules ![](data/chem/img/8YI.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-PEG / #4: Chemical | ChemComp-GOL / | #5: Chemical | #6: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.57 % |
---|---|
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 |
---|---|
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: 2.67→50.95 Å / Num. obs: 21089 / % possible obs: 99.84 % / Redundancy: 1 % / CC1/2: 0.96 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.89 |
Reflection shell | Resolution: 2.67→2.67 Å / Rmerge(I) obs: 0.45 / Num. unique obs: 2068 / CC1/2: 0.44 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4UY5 Resolution: 2.67→50.95 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.39 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 47.56 Å2 / Biso mean: 29.4438 Å2 / Biso min: 21.03 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.67→50.95 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Origin x: -22.245 Å / Origin y: -5.5358 Å / Origin z: 18.0802 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|