[English] 日本語
Yorodumi- PDB-3px2: Structure of TylM1 from Streptomyces fradiae H123N mutant in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3px2 | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of TylM1 from Streptomyces fradiae H123N mutant in complex with SAH and dTDP-Quip3N | ||||||
Components | N-methyltransferase | ||||||
Keywords | TRANSFERASE / SAM binding / N / N-dimethyltransferase / dTDP-Quip3N binding | ||||||
Function / homology | Function and homology information dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Streptomyces fradiae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Holden, H.M. / Carney, A.E. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Molecular Architecture of TylM1 from Streptomyces fradiae: An N,N-Dimethyltransferase Involved in the Production of dTDP-d-mycaminose . Authors: Carney, A.E. / Holden, H.M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3px2.cif.gz | 118.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3px2.ent.gz | 90.5 KB | Display | PDB format |
PDBx/mmJSON format | 3px2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/px/3px2 ftp://data.pdbj.org/pub/pdb/validation_reports/px/3px2 | HTTPS FTP |
---|
-Related structure data
Related structure data | 3pfgC 3pfhSC 3px3C C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 28375.697 Da / Num. of mol.: 2 / Mutation: H123N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces fradiae (bacteria) / Strain: ATCC 19609 / Gene: tylM1, tylMI(orf3*) / Plasmid: pET31b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P95748 #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.58 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 16% PEG 5000 monomethyl-ether, 2% 1,4-dioxane, 100mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Aug 6, 2010 / Details: Montell |
Radiation | Monochromator: nickel filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→77.1 Å / Num. all: 60958 / Num. obs: 60958 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 9.6 |
Reflection shell | Resolution: 1.65→1.75 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / Num. unique all: 8728 / Rsym value: 0.39 / % possible all: 83.4 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3PFH Resolution: 1.65→77.05 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.912 / SU B: 2.472 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.107 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.534 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.65→77.05 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.65→1.693 Å / Total num. of bins used: 20
|