+Open data
-Basic information
Entry | Database: PDB / ID: 6mjg | ||||||
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Title | Structure of dbOphMA in Complex with SAH and Methylated Peptide | ||||||
Components | fusion protein of dbOphMA and methylated peptide | ||||||
Keywords | BIOSYNTHETIC PROTEIN / Methyltransferase / borosin | ||||||
Function / homology | Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / methyltransferase activity / S-ADENOSYL-L-HOMOCYSTEINE / fusion protein of dbOphMA and methylated peptide Function and homology information | ||||||
Biological species | Dendrothele bispora CBS 962.96 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.123 Å | ||||||
Authors | Ongpipattanakul, C. / Nair, S.K. | ||||||
Funding support | United States, 1items
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Citation | Journal: ACS Chem. Biol. / Year: 2018 Title: Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis. Authors: Ongpipattanakul, C. / 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 | 6mjg.cif.gz | 91.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mjg.ent.gz | 71 KB | Display | PDB format |
PDBx/mmJSON format | 6mjg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/6mjg ftp://data.pdbj.org/pub/pdb/validation_reports/mj/6mjg | HTTPS FTP |
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-Related 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: 46222.512 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Mismatches are methylated Valine, methylated Isoleucine, methylated Glycine. The enzyme has a peptide sequence at the C-terminus that is not methylated until it is recombinantly expressed (sequence VISSVVA) Source: (gene. exp.) Dendrothele bispora CBS 962.96 (fungus) Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSY9*PLUS |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-ZN / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.52 % |
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Crystal grow | Temperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 mM SAH mixed 0.24 or 0.26 M NaF, 26% PEG3350, and 0.1 M Bis-tris propane at pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97872 A |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 28, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.123→75.79 Å / Num. obs: 25211 / % possible obs: 96.2 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.037 / Rrim(I) all: 0.072 / Net I/σ(I): 20.3 |
Reflection shell | Resolution: 2.123→2.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1166 / CC1/2: 0.8 / Rpim(I) all: 0.444 / Rrim(I) all: 0.783 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.123→25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.102 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.182 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.833 Å2
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Refinement step | Cycle: 1 / Resolution: 2.123→25 Å
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Refine LS restraints |
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