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- PDB-7rc6: Aeronamide N-methyltransferase, AerE, bound to modified peptide s... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7rc6 | ||||||
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Title | Aeronamide N-methyltransferase, AerE, bound to modified peptide substrate, AerA-DL,34 | ||||||
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![]() | TRANSFERASE/BIOSYNTHETIC PROTEIN / SAM-dependent / peptide cytotoxin / proteusin / BIOSYNTHETIC PROTEIN / TRANSFERASE-BIOSYNTHETIC PROTEIN complex | ||||||
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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 107.6 KB | Display | ![]() |
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PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 21.9 KB | Display | |
Data in CIF | ![]() | 34.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7rc2SC ![]() 7rc3C ![]() 7rc4C ![]() 7rc5C 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
#1: Protein | Mass: 42007.539 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: aerE / Production host: ![]() ![]() |
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#2: Protein/peptide | Mass: 3058.358 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: aerA / Production host: ![]() ![]() |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-SAH / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.88 % |
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Crystal grow | Temperature: 282 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 18% PEG 3350, 0.1 M sodium citrate pH 4.0, 0.2 M sodium citrate |
-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: Oct 7, 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: 1.71→67.575 Å / Num. obs: 58778 / % possible obs: 100 % / Redundancy: 14.8 % / CC1/2: 1 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.023 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.715→1.744 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.047 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2903 / CC1/2: 0.805 / Rpim(I) all: 0.327 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 7RC2 Resolution: 1.71→40.78 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.49 / 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: 79.81 Å2 / Biso mean: 24.0548 Å2 / Biso min: 10.79 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.71→40.78 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21
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