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- PDB-5ouf: Crystal structure of OphA-DeltaC6 mutant W400A in complex with Si... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ouf | ||||||
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Title | Crystal structure of OphA-DeltaC6 mutant W400A in complex with Sinefungin | ||||||
![]() | OphA peptide N-methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase | ||||||
Function / homology | Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / methyltransferase activity / BICARBONATE ION / THIOCYANATE ION / SINEFUNGIN / Peptide N-methyltransferase![]() | ||||||
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 | ![]() | 174.1 KB | Display | ![]() |
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PDB format | ![]() | 136.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 863.9 KB | Display | ![]() |
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Full document | ![]() | 867.5 KB | Display | |
Data in XML | ![]() | 17.9 KB | Display | |
Data in CIF | ![]() | 25.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5n0nC ![]() 5n0oSC ![]() 5n0pC ![]() 5n0qC ![]() 5n0rC ![]() 5n0sC ![]() 5n0tC ![]() 5n0uC ![]() 5n0vC ![]() 5n0wC ![]() 5n0xC ![]() 5n4iC ![]() 6gewC 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 on special symmetry positions |
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Components
#1: Protein | Mass: 44913.059 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-SFG / | ||
#3: Chemical | ChemComp-BCT / | ||
#4: Chemical | ChemComp-SCN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.55 Å3/Da / Density % sol: 65.31 % |
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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 8.5, 1.3-1.5 M sodium malonate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 27, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.7 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→49.55 Å / Num. obs: 70395 / % possible obs: 100 % / Redundancy: 7.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.7→1.73 Å / Redundancy: 7.7 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1.2 / CC1/2: 0.47 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N0O Resolution: 1.7→49.55 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.165 / SU ML: 0.058 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.074 / 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: 1.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.921 Å2
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Refinement step | Cycle: 1 / Resolution: 1.7→49.55 Å
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Refine LS restraints |
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