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Yorodumi- PDB-3pfg: X-Ray crystal structure the N,N-dimethyltransferase TylM1 from St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3pfg | ||||||
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Title | X-Ray crystal structure the N,N-dimethyltransferase TylM1 from Streptomyces fradiae in complex with SAM and dTDP-phenol | ||||||
Components | N-methyltransferase | ||||||
Keywords | TRANSFERASE / N / N-dimethyltransferase / SAM binding / dTDP-linked sugar 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: 1.349 Å | ||||||
Authors | Carney, A.E. / Holden, H.M. | ||||||
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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3pfg.cif.gz | 69.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3pfg.ent.gz | 49.3 KB | Display | PDB format |
PDBx/mmJSON format | 3pfg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/3pfg ftp://data.pdbj.org/pub/pdb/validation_reports/pf/3pfg | HTTPS FTP |
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-Related structure data
Related structure data | 3pfhC 3px2C 3px3C 3bxoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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: 28537.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylM1, tylMI(orf3*) / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P95748 |
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#2: Chemical | ChemComp-SAM / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-TLO / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.37 Å3/Da / Density % sol: 48.01 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 22% monomethylether poly(ethylene glycol) 5000, 2% isopropanol, 100mM MOPS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Mar 8, 2010 / Details: Montell |
Radiation | Monochromator: Ni Filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.349→100 Å / Num. all: 55697 / Num. obs: 55697 / % possible obs: 94.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.349→1.44 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.213 / Mean I/σ(I) obs: 2.6 / Num. unique all: 9141 / Rsym value: 0.213 / % possible all: 87.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3BXO Resolution: 1.349→100 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 0.881 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.057 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 16.587 Å2
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Refinement step | Cycle: LAST / Resolution: 1.349→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.349→1.384 Å / Total num. of bins used: 20
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