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Yorodumi- PDB-6cx6: The structure of an As(III) S-adenosylmethionine methyltransferas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cx6 | |||||||||
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Title | The structure of an As(III) S-adenosylmethionine methyltransferase with As(III) and S-adenosyl-L-homocysteine (SAH) | |||||||||
Components | Arsenic methyltransferase | |||||||||
Keywords | TRANSFERASE / methyltransferase | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Cyanidioschyzon sp. 5508 (eukaryote) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å | |||||||||
Authors | Packianathan, C. / Kandavelu, P. / Rosen, B.P. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Biochemistry / Year: 2018 Title: The Structure of an As(III) S-Adenosylmethionine Methyltransferase with 3-Coordinately Bound As(III) Depicts the First Step in Catalysis. Authors: Packianathan, C. / Kandavelu, P. / Rosen, B.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6cx6.cif.gz | 145.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cx6.ent.gz | 112.6 KB | Display | PDB format |
PDBx/mmJSON format | 6cx6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/6cx6 ftp://data.pdbj.org/pub/pdb/validation_reports/cx/6cx6 | HTTPS FTP |
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-Related structure data
Related structure data | 4fs8S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 41800.176 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Cyanidioschyzon sp. 5508 (eukaryote) / Gene: arsM / Plasmid: pET28(a) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C0JV69, EC: 2.1.1.137 #2: Chemical | #3: Chemical | #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: 2.71 Å3/Da / Density % sol: 54.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.4 M potassium phosphate dibasic, 0.4 M sodium phosphate monobasic, 0.1 M imidazole, pH 8.0, 0.2 M sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 18, 2013 / Details: Mirror |
Radiation | Monochromator: double crystal Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.84→100 Å / Num. obs: 22216 / % possible obs: 99.4 % / Redundancy: 18.7 % / Biso Wilson estimate: 50.2 Å2 / Rpim(I) all: 0.028 / Rsym value: 0.119 / Net I/σ(I): 22 |
Reflection shell | Resolution: 2.84→2.94 Å / Redundancy: 15.2 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2058 / Rpim(I) all: 0.16 / Rsym value: 0.69 / % possible all: 95.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4FS8 Resolution: 2.84→48.87 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.873 / SU B: 17.346 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R: 5.09 / ESU R Free: 0.421 / 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: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 62.888 Å2
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Refinement step | Cycle: 1 / Resolution: 2.84→48.87 Å
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Refine LS restraints |
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