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Yorodumi- PDB-8t1t: Structure of the alpha-N-methyltransferase (SonM) and RiPP precur... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8t1t | ||||||
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Title | Structure of the alpha-N-methyltransferase (SonM) and RiPP precursor (SonA with QSY deletion) heteromeric complex (bound to SAM) | ||||||
Components |
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Keywords | TRANSFERASE / alpha-N-methyltransferase / borosin / natural products | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Shewanella oneidensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å | ||||||
Authors | Crone, K.K. / Jomori, T. / Miller, F.S. / Gralnick, J. / Elias, M. / Freeman, M.F. | ||||||
Funding support | United States, 1items
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Citation | Journal: Rsc Chem Biol / Year: 2023 Title: RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin alpha- N -methylated peptide natural product. Authors: Crone, K.K. / Jomori, T. / Miller, F.S. / Gralnick, J.A. / 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 | 8t1t.cif.gz | 285.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t1t.ent.gz | 226.7 KB | Display | PDB format |
PDBx/mmJSON format | 8t1t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t1/8t1t ftp://data.pdbj.org/pub/pdb/validation_reports/t1/8t1t | HTTPS FTP |
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-Related structure data
Related structure data | 8t1sC 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
#1: Protein | Mass: 29068.326 Da / Num. of mol.: 2 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: 8404.297 Da / Num. of mol.: 2 / Mutation: Deletion of sequence QSY 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: Chemical | #4: Chemical | ChemComp-ZN / | #5: 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: 45.59 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 240 mM sodium malonate pH 5-5.5, 8-12% PEG 3350 at a 1-1 or 2-1 ratio of protein to mother liquor. Protein concentration is 20mg/mL |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Mar 11, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→46.13 Å / Num. obs: 87728 / % possible obs: 92.1 % / Redundancy: 2.8 % / CC1/2: 0.998 / Rrim(I) all: 0.054 / Net I/σ(I): 12.53 |
Reflection shell | Resolution: 1.55→1.65 Å / Num. unique obs: 15117 / CC1/2: 0.667 / Rrim(I) all: 0.715 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→46.13 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.962 / SU B: 4.73 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.254 Å2
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Refinement step | Cycle: 1 / Resolution: 1.55→46.13 Å
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