+Open data
-Basic information
Entry | Database: PDB / ID: 3ou6 | ||||||
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Title | DhpI-SAM complex | ||||||
Components | SAM-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / O-methyltransferase / SAM | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces luridus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å | ||||||
Authors | Bae, B. / Nair, S.K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2010 Title: Characterization and structure of DhpI, a phosphonate O-methyltransferase involved in dehydrophos biosynthesis. Authors: Lee, J.H. / Bae, B. / Kuemin, M. / Circello, B.T. / Metcalf, W.W. / Nair, S.K. / van der Donk, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ou6.cif.gz | 189.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ou6.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ou6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/3ou6 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/3ou6 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24605.250 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces luridus (bacteria) / Gene: dhpI / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: D7PC21 #2: Chemical | ChemComp-SAM / #3: Chemical | ChemComp-SO4 / #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: 3.41 Å3/Da / Density % sol: 63.97 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M Ammonium sulphate, 100 mM Tris-HCl pH=8.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-D |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 26, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.3→46.47 Å / Num. all: 60586 / Num. obs: 60586 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 39.8 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 17.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 7.7 / Num. unique all: 6000 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.916 / SU B: 5.341 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.791 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.359 Å / Total num. of bins used: 20
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