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Yorodumi- PDB-6fny: CRYSTAL STRUCTURE OF A CHOLINE SULFATASE FROM SINORHIZOBIUM MELLILOTI -
+Open data
-Basic information
Entry | Database: PDB / ID: 6fny | |||||||||
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Title | CRYSTAL STRUCTURE OF A CHOLINE SULFATASE FROM SINORHIZOBIUM MELLILOTI | |||||||||
Components | Choline-sulfatase | |||||||||
Keywords | HYDROLASE | |||||||||
Function / homology | Function and homology information choline biosynthetic process / choline-sulfatase / choline-sulfatase activity / metal ion binding Similarity search - Function | |||||||||
Biological species | Sinorhizobium meliloti 1021 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å | |||||||||
Authors | Valkov, E. / Van Loo, B. / Hollfelder, F. / Hyvonen, M. | |||||||||
Funding support | United Kingdom, 1items
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Citation | Journal: J. Mol. Biol. / Year: 2018 Title: Structural and Mechanistic Analysis of the Choline Sulfatase from Sinorhizobium melliloti: A Class I Sulfatase Specific for an Alkyl Sulfate Ester. Authors: van Loo, B. / Schober, M. / Valkov, E. / Heberlein, M. / Bornberg-Bauer, E. / Faber, K. / Hyvonen, M. / Hollfelder, F. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6fny.cif.gz | 830.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6fny.ent.gz | 706.6 KB | Display | PDB format |
PDBx/mmJSON format | 6fny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fn/6fny ftp://data.pdbj.org/pub/pdb/validation_reports/fn/6fny | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 58809.789 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Sinorhizobium meliloti 1021 / Gene: betC, R00949, SMc00127 / Production host: Escherichia coli (E. coli) / References: UniProt: O69787, choline-sulfatase #2: Chemical | ChemComp-CA / #3: 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: 3.67 Å3/Da / Density % sol: 66.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 800 MM SODIUM CITRATE, 100 MM IMIDAZOLE (PH 8.0) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 21, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 2.79→95.55 Å / Num. obs: 167730 / % possible obs: 99.4 % / Observed criterion σ(I): 1.4 / Redundancy: 3.9 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 14.7 |
Reflection shell | Resolution: 2.79→2.84 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.4 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.79→88.55 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.99 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.79→88.55 Å
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Refine LS restraints |
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LS refinement shell |
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