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Yorodumi- PDB-7ltf: Structure of the alpha-N-methyltransferase (SonM mutant Y58F) and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ltf | ||||||
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Title | Structure of the alpha-N-methyltransferase (SonM mutant Y58F) and RiPP precursor (SonA) heteromeric complex (no cofactor) | ||||||
Components |
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Keywords | TRANSFERASE / posttranslational modifications / ribosomally synthesized and posttranslationally modified peptides / alpha-N-methyltransferase / borosin / SAM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Miller, F.S. / Crone, K.K. / Jensen, M.R. / Shaw, S. / Harcombe, W.R. / Elias, M. / Freeman, M.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Conformational rearrangements enable iterative backbone N-methylation in RiPP biosynthesis. Authors: Miller, F.S. / Crone, K.K. / Jensen, M.R. / Shaw, S. / Harcombe, W.R. / Elias, M.H. / Freeman, M.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ltf.cif.gz | 152.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ltf.ent.gz | 117.6 KB | Display | PDB format |
PDBx/mmJSON format | 7ltf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lt/7ltf ftp://data.pdbj.org/pub/pdb/validation_reports/lt/7ltf | HTTPS FTP |
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-Related structure data
Related structure data | 7ltcC 7lteC 7lthC 7ltrC 7ltsC 5n0pS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29052.326 Da / Num. of mol.: 2 / Mutation: Y58F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1478 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW3 #2: Protein | Mass: 7850.653 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: SO_1479 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8EGW2 #3: Water | ChemComp-HOH / | 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: 2.26 Å3/Da / Density % sol: 45.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: Proteins were concentrated at 20 mg/mL and crystallized at pH ranging between 5.5-7 and using PEG 3,350 (0-20%) as precipitant |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.033167 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033167 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→58.8 Å / Num. obs: 33041 / % possible obs: 99.1 % / Redundancy: 4.61 % / CC1/2: 0.991 / Net I/σ(I): 15.48 |
Reflection shell | Resolution: 2.2→2.3 Å / Num. unique obs: 4031 / CC1/2: 0.978 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N0P Resolution: 2.2→58.8 Å / Cross valid method: THROUGHOUT
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Displacement parameters | Biso max: 125.31 Å2 / Biso mean: 26.4867 Å2 / Biso min: 8.88 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→58.8 Å
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