+Open data
-Basic information
Entry | Database: PDB / ID: 5f8c | |||||||||
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Title | Rv2258c-unbound | |||||||||
Components | Methyltransferase | |||||||||
Keywords | TRANSFERASE / methyltransferase / Class I / sinefungin / S-adenosyl-L-homocysteine | |||||||||
Function / homology | Function and homology information Transferases; Transferring one-carbon groups; Methyltransferases / peptidoglycan-based cell wall / methyltransferase activity / methylation / cellular response to hypoxia / plasma membrane Similarity search - Function | |||||||||
Biological species | Mycobacterium tuberculosis H37Rv (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å | |||||||||
Authors | Im, H.N. / Suh, S.W. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Struct.Biol. / Year: 2016 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5f8c.cif.gz | 220.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5f8c.ent.gz | 181.7 KB | Display | PDB format |
PDBx/mmJSON format | 5f8c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/5f8c ftp://data.pdbj.org/pub/pdb/validation_reports/f8/5f8c | HTTPS FTP |
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-Related structure data
-Links
-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.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: Rv2258c, LH57_12310 / Production host: Escherichia coli (E. coli) / References: UniProt: O53532 #2: Chemical | ChemComp-GOL / #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: 3.26 Å3/Da / Density % sol: 62.3 % |
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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: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.92019 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92019 Å / Relative weight: 1 |
Reflection | Resolution: 1.83→27.25 Å / Num. obs: 127941 / % possible obs: 99.9 % / Redundancy: 4.1 % / Net I/σ(I): 28.7 |
Reflection shell | Resolution: 1.83→1.86 Å / Mean I/σ(I) obs: 2.9 |
-Processing
Software |
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Refinement | Resolution: 1.83→27.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.02 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.114 / 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: 33.159 Å2
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Refinement step | Cycle: 1 / Resolution: 1.83→27.25 Å
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