+Open data
-Basic information
Entry | Database: PDB / ID: 3ou2 | ||||||
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Title | DhpI-SAH complex structure | ||||||
Components | SAM-dependent methyltransferase | ||||||
Keywords | TRANSFERASE / O-methyltransferase / SAH | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces luridus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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 | 3ou2.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ou2.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ou2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ou/3ou2 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/3ou2 | HTTPS FTP |
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-Related structure data
Related structure data | 3ou6SC 3ou7C S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 24605.250 Da / Num. of mol.: 1 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 |
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#2: Chemical | ChemComp-SAH / |
#3: 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: 2.36 Å3/Da / Density % sol: 47.97 % |
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Crystal grow | Temperature: 273 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.6 M Ammonium sulphate, 100 mM Tric-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 / Wavelength: 0.9796 Å |
Detector | Type: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 10, 2008 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→33.3 Å / Num. all: 36451 / Num. obs: 36451 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rsym value: 0.047 / Net I/σ(I): 38.1 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3.9 / Num. unique all: 3458 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3OU6 Resolution: 1.5→25 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.346 / SU ML: 0.051 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.078 / 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: 22.509 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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