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Yorodumi- PDB-5n0v: Crystal structure of OphA-DeltaC6 mutant Y76F in complex with SAH -
+Open data
-Basic information
Entry | Database: PDB / ID: 5n0v | ||||||
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Title | Crystal structure of OphA-DeltaC6 mutant Y76F in complex with SAH | ||||||
Components | Peptide N-methyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase | ||||||
Function / homology | Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / methyltransferase activity / S-ADENOSYL-L-HOMOCYSTEINE / Peptide N-methyltransferase Function and homology information | ||||||
Biological species | Omphalotus olearius (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 | 5n0v.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n0v.ent.gz | 262.8 KB | Display | PDB format |
PDBx/mmJSON format | 5n0v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5n0v_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5n0v_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 5n0v_validation.xml.gz | 32.8 KB | Display | |
Data in CIF | 5n0v_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/5n0v ftp://data.pdbj.org/pub/pdb/validation_reports/n0/5n0v | HTTPS FTP |
-Related structure data
Related structure data | 5n0nC 5n0oSC 5n0pC 5n0qC 5n0rC 5n0sC 5n0tC 5n0uC 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: 44984.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Omphalotus olearius (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2R2JFI1*PLUS #2: Chemical | #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: 3.73 Å3/Da / Density % sol: 67 % |
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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: I03 / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 21, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.91→85.62 Å / Num. obs: 100787 / % possible obs: 99.9 % / Redundancy: 7.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.6 |
Reflection shell | Resolution: 1.91→1.94 Å / Rmerge(I) obs: 1.488 / CC1/2: 0.578 / % possible all: 97.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5N0O Resolution: 1.91→85.62 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 8.172 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.121 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.078 Å2
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Refinement step | Cycle: 1 / Resolution: 1.91→85.62 Å
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Refine LS restraints |
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