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Yorodumi- PDB-7rc6: Aeronamide N-methyltransferase, AerE, bound to modified peptide s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7rc6 | ||||||
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Title | Aeronamide N-methyltransferase, AerE, bound to modified peptide substrate, AerA-DL,34 | ||||||
Components |
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Keywords | 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 Function and homology information | ||||||
Biological species | Microvirgula aerodenitrificans DSM 15089 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å | ||||||
Authors | Cogan, D.P. / Reyes, R. / Nair, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7rc6.cif.gz | 107.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rc6.ent.gz | 77.6 KB | Display | PDB format |
PDBx/mmJSON format | 7rc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/7rc6 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rc6 | HTTPS FTP |
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-Related structure data
Related structure data | 7rc2SC 7rc3C 7rc4C 7rc5C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Microvirgula aerodenitrificans DSM 15089 (bacteria) Gene: aerE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A329B7M1 |
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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.) Microvirgula aerodenitrificans DSM 15089 (bacteria) Gene: aerA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) |
#3: Chemical | ChemComp-NA / |
#4: Chemical | ChemComp-SAH / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å |
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 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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