+Open data
-Basic information
Entry | Database: PDB / ID: 5n0o | |||||||||
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Title | Crystal structure of Seleno-OphA-DeltaC18 in complex with SAM | |||||||||
Components | (Peptide N-methyltransferase) x 2 | |||||||||
Keywords | TRANSFERASE / methyltransferase | |||||||||
Function / homology | Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / methyltransferase activity / L-HOMOSERINE / S-ADENOSYLMETHIONINE / Peptide N-methyltranferase Function and homology information | |||||||||
Biological species | Omphalotus olearius (fungus) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.44 Å | |||||||||
Authors | Naismith, J.H. / Song, 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 | 5n0o.cif.gz | 338.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n0o.ent.gz | 274.3 KB | Display | PDB format |
PDBx/mmJSON format | 5n0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0o ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0o | HTTPS FTP |
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-Related structure data
Related structure data | 5n0nC 5n0pC 5n0qC 5n0rC 5n0sC 5n0tC 5n0uC 5n0vC 5n0wC 5n0xC 5n4iC 5oufC 6gewC 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
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 44292.602 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: A0A2R2JFH7*PLUS |
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#2: Protein | Mass: 44308.602 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: A0A2R2JFH7*PLUS |
-Non-polymers , 4 types, 820 molecules
#3: Chemical | #4: Chemical | ChemComp-EDO / #5: Chemical | ChemComp-HSE / | #6: 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: 2.64 Å3/Da / Density % sol: 53.49 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2 M NaCl, 0.1 M Bis-Tris pH 6.0 and 20% PEG 3350 |
-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: Aug 1, 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: 1.437→78.08 Å / Num. obs: 169405 / % possible obs: 100 % / Redundancy: 11.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 1.437→1.441 Å / Redundancy: 11.5 % / Rmerge(I) obs: 1.142 / CC1/2: 0.751 / % possible all: 95.9 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.44→78.08 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.109 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.056 / 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: 25.913 Å2
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Refinement step | Cycle: 1 / Resolution: 1.44→78.08 Å
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