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Open data
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Basic information
Entry | Database: PDB / ID: 7rc3 | ||||||
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Title | Aeronamide N-methyltransferase, AerE (Y137F) | ||||||
![]() | 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 / ASPARTIC ACID / TRIETHYLENE GLYCOL / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase family protein![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cogan, D.P. / Reyes, R. / Nair, S.K. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 103.7 KB | Display | ![]() |
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PDB format | ![]() | 74.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7rc2SC ![]() 7rc4C ![]() 7rc5C ![]() 7rc6C S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 41991.539 Da / Num. of mol.: 1 / Mutation: Y137F Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() |
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-Non-polymers , 8 types, 463 molecules ![](data/chem/img/ASP.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PG4.gif)
![](data/chem/img/PGE.gif)
![](data/chem/img/P6G.gif)
![](data/chem/img/SAH.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ASP / | ||
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#3: Chemical | ChemComp-PG4 / | ||
#4: Chemical | ChemComp-PGE / | ||
#5: Chemical | ChemComp-P6G / | ||
#6: Chemical | ChemComp-SAH / | ||
#7: Chemical | ChemComp-CA / | ||
#8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.06 % |
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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 |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.526→67.287 Å / Num. obs: 81532 / % possible obs: 100 % / Redundancy: 17 % / CC1/2: 1 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.023 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.526→1.553 Å / Redundancy: 15.6 % / Rmerge(I) obs: 1.296 / Num. unique obs: 4014 / CC1/2: 0.776 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7RC2 Resolution: 1.53→19.52 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 16.82 / 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: 64.4 Å2 / Biso mean: 20.6858 Å2 / Biso min: 10.74 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.53→19.52 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29 / % reflection obs: 100 %
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