+
Open data
-
Basic information
Entry | Database: PDB / ID: 7rc4 | ||||||
---|---|---|---|---|---|---|---|
Title | Aeronamide N-methyltransferase, AerE (D141A) | ||||||
![]() | Methyltransferase family protein | ||||||
![]() | TRANSFERASE / SAM-dependent / peptide cytotoxin / proteusin | ||||||
Function / homology | Methyltransferase small domain / Methyltransferase small domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cogan, D.P. / Reyes, R. / Nair, S.K. | ||||||
![]() | ![]() Title: Structure and mechanism for iterative amide N -methylation in the biosynthesis of channel-forming peptide cytotoxins. Authors: Cogan, D.P. / Bhushan, A. / Reyes, R. / Zhu, L. / Piel, J. / Nair, S.K. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 100.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 72.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 19.4 KB | Display | |
Data in CIF | ![]() | 29.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rc2SC ![]() 7rc3C ![]() 7rc5C ![]() 7rc6C S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
-
Assembly
Deposited unit | ![]()
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||
Unit cell |
| |||||||||
Components on special symmetry positions |
|
-
Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41963.527 Da / Num. of mol.: 1 / Mutation: D141A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
---|
-Non-polymers , 6 types, 387 molecules ![](data/chem/img/SAH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-SAH / | ||||||||
---|---|---|---|---|---|---|---|---|---|
#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-P6G / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.86 % |
---|---|
Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 37.5% PEG 300, 0.1 M sodium cacodylate pH 6.5, 0.2 M calcium acetate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Nov 6, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.659→67.199 Å / Num. obs: 61591 / % possible obs: 97.2 % / Redundancy: 17.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.025 / Net I/σ(I): 15.5 |
Reflection shell | Resolution: 1.659→1.688 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.186 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3133 / CC1/2: 0.876 / Rpim(I) all: 0.331 / % possible all: 100 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 7RC2 Resolution: 1.66→40.41 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.03 / 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: 72 Å2 / Biso mean: 23.9829 Å2 / Biso min: 13.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.66→40.41 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
|