+Open data
-Basic information
Entry | Database: PDB / ID: 6tsc | ||||||
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Title | OphMA I407P complex with SAH | ||||||
Components |
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Keywords | TRANSFERASE / Peptide bond N-methyltransferase | ||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | Omphalotus olearius (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Song, H. / Naismith, J.H. | ||||||
Citation | Journal: Acs Chem.Biol. / Year: 2020 Title: Substrate Plasticity of a Fungal Peptide alpha-N-Methyltransferase. Authors: Song, H. / Fahrig-Kamarauskaite, J.R. / Matabaro, E. / Kaspar, H. / Shirran, S.L. / Zach, C. / Pace, A. / Stefanov, B.A. / Naismith, J.H. / Kunzler, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tsc.cif.gz | 169.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tsc.ent.gz | 133.1 KB | Display | PDB format |
PDBx/mmJSON format | 6tsc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ts/6tsc ftp://data.pdbj.org/pub/pdb/validation_reports/ts/6tsc | HTTPS FTP |
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-Related structure data
Related structure data | 6qzyC 6qzzC 6r00C 5n0oS S: Starting model for refinement C: citing same article (ref.) |
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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: 45618.789 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFI5 |
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#2: Protein/peptide | Mass: 1254.519 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A2R2JFH9*PLUS |
#3: Chemical | ChemComp-SAH / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.15 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.3-0.4 M KSCN, 0.1 M Bicine pH 8-9, 1.8-2.5 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 6, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→52.33 Å / Num. obs: 38116 / % possible obs: 100 % / Redundancy: 11.1 % / CC1/2: 1 / Rrim(I) all: 0.058 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.19→2.23 Å / Redundancy: 10.9 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1877 / CC1/2: 0.9 / Rrim(I) all: 2.088 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N0O Resolution: 2.19→52.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 23.313 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.163 / ESU R Free: 0.149 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 192.48 Å2 / Biso mean: 99.841 Å2 / Biso min: 60.55 Å2
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Refinement step | Cycle: final / Resolution: 2.19→52.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.19→2.247 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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