+Open data
-Basic information
Entry | Database: PDB / ID: 3bxo | ||||||
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Title | Crystal Structure of Streptomyces venezuelae DesVI | ||||||
Components | N,N-dimethyltransferase | ||||||
Keywords | TRANSFERASE / methyltransferase / desosamine / sugar / carbohydrate / antibiotic / SAM / Adomet | ||||||
Function / homology | Function and homology information dTDP-3-amino-3,4,6-trideoxy-alpha-D-glucopyranose N,N-dimethyltransferase / S-adenosylmethionine-dependent methyltransferase activity / antibiotic biosynthetic process / methylation / protein homodimerization activity Similarity search - Function | ||||||
Biological species | Streptomyces venezuelae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MAD, molecular replacement / MAD / molecular replacement / Resolution: 2 Å | ||||||
Authors | Holden, H.M. / Burgie, E.S. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Three-Dimensional Structure of DesVI from Streptomyces venezuelae: A Sugar N,N-Dimethyltransferase Required for dTDP-Desosamine Biosynthesis. Authors: Burgie, E.S. / 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 | 3bxo.cif.gz | 121.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bxo.ent.gz | 92.6 KB | Display | PDB format |
PDBx/mmJSON format | 3bxo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/3bxo ftp://data.pdbj.org/pub/pdb/validation_reports/bx/3bxo | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 26208.246 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Strain: ATCC no. 15,439 / Gene: desVI / Plasmid: pET28b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: Q9ZGH6 #2: Chemical | #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: 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: 2.87 Å3/Da / Density % sol: 57.22 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 5000 monomethyl ether, NaCl, S-adenosylmethionine, UDP-benzene, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Sep 18, 2007 / Details: Montel optics |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 40490 / Num. obs: 36362 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rsym value: 0.084 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 5470 / Rsym value: 0.254 / % possible all: 76.5 |
-Phasing
Phasing |
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-Processing
Software |
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Refinement | Method to determine structure: MAD, molecular replacement Starting model: Selenomethionine enriched DesVI model from MAD phasing Resolution: 2→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.391 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→30 Å
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Refine LS restraints |
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