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Open data
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Basic information
Entry | Database: PDB / ID: 6gew | ||||||
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Title | OphA Y63F-sinefungin complex | ||||||
![]() | OphA | ||||||
![]() | TRANSFERASE / Peptide N-transferase | ||||||
Function / homology | ![]() Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / methylation Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Song, H. / Naismith, J.H. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 166.7 KB | Display | ![]() |
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PDB format | ![]() | 131.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 15.8 KB | Display | |
Data in CIF | ![]() | 20.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n0nC ![]() 5n0oSC ![]() 5n0pC ![]() 5n0qC ![]() 5n0rC ![]() 5n0sC ![]() 5n0tC ![]() 5n0uC ![]() 5n0vC ![]() 5n0wC ![]() 5n0xC ![]() 5n4iC ![]() 5oufC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 44998.164 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-SAH / |
#3: Chemical | ChemComp-SFG / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 4.06 Å3/Da / Density % sol: 69.68 % |
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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, 1.7-2.0 M Sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→77.76 Å / Num. obs: 43488 / % possible obs: 100 % / Redundancy: 10.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 11 % / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 2110 / CC1/2: 0.556 / % possible all: 98.64 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N0O Resolution: 2.1→77.76 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.953 / SU B: 20.221 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 90.275 Å2
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Refinement step | Cycle: 1 / Resolution: 2.1→77.76 Å
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Refine LS restraints |
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