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Yorodumi- PDB-4oqd: Crystal structure of the tylM1 N,N-dimethyltransferase in complex... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oqd | ||||||
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Title | Crystal structure of the tylM1 N,N-dimethyltransferase in complex with SAH and TDP-Qui3NMe2 | ||||||
Components | dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase | ||||||
Keywords | TRANSFERASE / SAM methyltransferase / N-methyltransferase / S-adenosylmethionine | ||||||
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 / SYNCHROTRON / PHASER / Resolution: 1.6 Å | ||||||
Authors | Thoden, J.B. / Holden, H.M. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Production of a novel N-monomethylated dideoxysugar. Authors: Thoden, J.B. / 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 | 4oqd.cif.gz | 212.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oqd.ent.gz | 169.8 KB | Display | PDB format |
PDBx/mmJSON format | 4oqd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oq/4oqd ftp://data.pdbj.org/pub/pdb/validation_reports/oq/4oqd | HTTPS FTP |
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-Related structure data
Related structure data | 4oqeC 3pfhS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 28537.885 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: tylM1, tylMI / Plasmid: pET31 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) References: UniProt: P95748, dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase #2: Chemical | ChemComp-SAH / #3: Chemical | ChemComp-QDM / #4: 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: 2.28 Å3/Da / Density % sol: 46.14 % |
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Crystal grow | Temperature: 293 K / Method: batch / pH: 9 Details: 15-20% PEG3400, 200 mM sodium chloride, 5 mM S-adenosylhomocysteine, 10 mM TDP-3-N,N-dimethylamino-3,6-dideoxyglucose, pH 9, batch, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.98789 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 12, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98789 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 123048 / Num. obs: 123048 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 43.2 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 4.3 / Num. unique all: 5330 / Rsym value: 0.176 / % possible all: 79.6 |
-Processing
Software |
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Refinement | Method to determine structure: PHASER Starting model: PDB ENTRY 3PFH Resolution: 1.6→41.24 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.292 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.095 / ESU R Free: 0.096 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.063 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→41.24 Å
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