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Yorodumi- PDB-5n0n: Crystal structure of OphA-DeltaC6 mutant Y63F in complex with SAM -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n0n | ||||||
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Title | Crystal structure of OphA-DeltaC6 mutant Y63F in complex with SAM | ||||||
Components | Peptide N-methyltransferase | ||||||
Keywords | TRANSFERASE / 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: 1.76 Å | ||||||
Authors | Song, H. / Naismith, J.H. | ||||||
Citation | Journal: Sci Adv / Year: 2018 Title: A molecular mechanism for the enzymatic methylation of nitrogen atoms within peptide bonds. Authors: Song, H. / van der Velden, N.S. / Shiran, S.L. / Bleiziffer, P. / Zach, C. / Sieber, R. / Imani, A.S. / Krausbeck, F. / Aebi, M. / Freeman, M.F. / Riniker, S. / Kunzler, M. / Naismith, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5n0n.cif.gz | 179.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n0n.ent.gz | 141.9 KB | Display | PDB format |
PDBx/mmJSON format | 5n0n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n0n_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 5n0n_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 5n0n_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 5n0n_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0n ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0n | HTTPS FTP |
-Related structure data
Related structure data | 5n0oSC 5n0pC 5n0qC 5n0rC 5n0sC 5n0tC 5n0uC 5n0vC 5n0wC 5n0xC 5n4iC 5oufC 6gewC 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: 45028.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFH4*PLUS | ||
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#2: Chemical | ChemComp-SAH / | ||
#3: Chemical | ChemComp-EDT / {[-( | ||
#4: Chemical | #5: 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: 3.75 Å3/Da / Density % sol: 34.47 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop Details: 0.3-0.4 M KSCN, 1.5-1.9 M sodium malonate and 0.1 M bicine pH 9.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9281 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 25, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9281 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→82.67 Å / Num. obs: 67412 / % possible obs: 99.5 % / Redundancy: 5.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.76→1.79 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.791 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N0O Resolution: 1.76→82.67 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 4.068 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.083 / 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: 43.589 Å2
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Refinement step | Cycle: 1 / Resolution: 1.76→82.67 Å
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Refine LS restraints |
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