+Open data
-Basic information
Entry | Database: PDB / ID: 6mjf | ||||||
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Title | Catalytic Domain of dbOphMA | ||||||
Components | dbOphM | ||||||
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 / dbOphM Function and homology information | ||||||
Biological species | Dendrothele bispora CBS 962.96 (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.198 Å | ||||||
Authors | Ongpipatanakul, 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 | 6mjf.cif.gz | 445.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mjf.ent.gz | 364 KB | Display | PDB format |
PDBx/mmJSON format | 6mjf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/6mjf ftp://data.pdbj.org/pub/pdb/validation_reports/mj/6mjf | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 42804.680 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dendrothele bispora CBS 962.96 (fungus) Production host: Escherichia coli (E. coli) / References: UniProt: A0A452CSY8*PLUS #2: Chemical | ChemComp-SAH / #3: Water | ChemComp-HOH / | |
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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 % / Description: Sheets. |
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Crystal grow | Temperature: 282.15 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 2 mM SAH, 0.24 or 0.26 M NaF, 20- 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: 0.97911 Å |
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: 0.97911 Å / Relative weight: 1 |
Reflection | Resolution: 2.198→94.867 Å / Num. obs: 113414 / % possible obs: 99 % / Redundancy: 5.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.069 / Rsym value: 0.122 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.198→2.205 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1163 / CC1/2: 0.824 / Rpim(I) all: 0.498 / Rrim(I) all: 0.885 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.198→45.641 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 28.94 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.198→45.641 Å
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Refine LS restraints |
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LS refinement shell |
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