+Open data
-Basic information
Entry | Database: PDB / ID: 7rc4 | ||||||
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Title | Aeronamide N-methyltransferase, AerE (D141A) | ||||||
Components | Methyltransferase family protein | ||||||
Keywords | 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 Function and homology information | ||||||
Biological species | Microvirgula aerodenitrificans DSM 15089 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 | 7rc4.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7rc4.ent.gz | 72.7 KB | Display | PDB format |
PDBx/mmJSON format | 7rc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rc/7rc4 ftp://data.pdbj.org/pub/pdb/validation_reports/rc/7rc4 | HTTPS FTP |
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-Related structure data
Related structure data | 7rc2SC 7rc3C 7rc5C 7rc6C 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
-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.) Microvirgula aerodenitrificans DSM 15089 (bacteria) Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A329B7M1 |
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-Non-polymers , 6 types, 387 molecules
#2: Chemical | ChemComp-SAH / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-CA / | #5: Chemical | ChemComp-PG4 / | #6: Chemical | ChemComp-P6G / | #7: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.14 Å3/Da / Density % sol: 60.86 % |
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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: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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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: 72 Å2 / Biso mean: 23.9829 Å2 / Biso min: 13.42 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.66→40.41 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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