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Open data
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Basic information
Entry | Database: PDB / ID: 5f8e | ||||||
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Title | Rv2258c-SAH | ||||||
![]() | Methyltransferase | ||||||
![]() | TRANSFERASE / methyltransferase / Class I / sinefungin / S-adenosyl-L-homocysteine / complex | ||||||
Function / homology | ![]() peptidoglycan-based cell wall / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / cellular response to hypoxia / methylation / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Im, H.N. / Suh, S.W. | ||||||
![]() | ![]() Title: Crystal structure of Rv2258c from Mycobacterium tuberculosis H37Rv, an S-adenosyl-l-methionine-dependent methyltransferase Authors: Im, H.N. / Kim, H.S. / An, D.R. / Jang, J.Y. / Kim, J. / Yoon, H.J. / Yang, J.K. / Suh, S.W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 204.9 KB | Display | ![]() |
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PDB format | ![]() | 170.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40490.605 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: H37Rv / Gene: Rv2258c, LH57_12310 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.27 Å3/Da / Density % sol: 62.4 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: sodium malonate, PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→50 Å / Num. obs: 32186 / % possible obs: 99.9 % / Redundancy: 4.1 % / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 2.9→2.95 Å / Mean I/σ(I) obs: 2.8 |
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Processing
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Refinement | Resolution: 2.9→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.886 / SU B: 22.013 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.409 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 110.06 Å2 / Biso mean: 46.499 Å2 / Biso min: 4.27 Å2
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Refinement step | Cycle: final / Resolution: 2.9→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.975 Å / Total num. of bins used: 20
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