[English] 日本語
Yorodumi- PDB-1wg8: Crystal structure of a predicted S-adenosylmethionine-dependent m... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1wg8 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of a predicted S-adenosylmethionine-dependent methyltransferase TT1512 from Thermus thermophilus HB8. | ||||||
Components | predicted S-adenosylmethionine-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / S-adenosyl-methyltransferase / mraW / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics | ||||||
Function / homology | Function and homology information 16S rRNA (cytosine1402-N4)-methyltransferase / rRNA (cytosine-N4-)-methyltransferase activity / rRNA base methylation / cytoplasm Similarity search - Function | ||||||
Biological species | Thermus thermophilus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI) | ||||||
Citation | Journal: To be Published Title: Crystal structure of a predicted S-adenosylmethionine-dependent methyltransferase TT1512 from Thermus thermophilus HB8 at 2.0 Ang. resolution. Authors: Kishishita, S. / Murayama, K. / Shirouzu, M. / Yokoyama, S. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1wg8.cif.gz | 123.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1wg8.ent.gz | 96.9 KB | Display | PDB format |
PDBx/mmJSON format | 1wg8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wg/1wg8 ftp://data.pdbj.org/pub/pdb/validation_reports/wg/1wg8 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1n2xS S: Starting model for refinement |
---|---|
Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 31223.180 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TT1512 / Plasmid: pET11b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: Q5SJD8, Transferases; Transferring one-carbon groups; Methyltransferases #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 51.2 % |
---|---|
Crystal grow | Temperature: 293 K / Method: concentration / pH: 8 / Details: NaCl, DTT, pH 8.0, Concentration, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→20 Å / Num. obs: 42752 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.84 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.034 / Net I/σ(I): 39.5 |
Reflection shell | Resolution: 2→2.07 Å / Mean I/σ(I) obs: 5.15 / Rsym value: 0.263 / % possible all: 99.9 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1N2X Resolution: 2→19.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 703863.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 67.0347 Å2 / ksol: 0.416041 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.7 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→19.92 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
|