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Yorodumi- PDB-3ckl: Crystal structure of human cytosolic sulfotransferase SULT1B1 in ... -
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-Basic information
Entry | Database: PDB / ID: 3ckl | ||||||
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Title | Crystal structure of human cytosolic sulfotransferase SULT1B1 in complex with PAP and resveratrol | ||||||
Components | Sulfotransferase family cytosolic 1B member 1 | ||||||
Keywords | TRANSFERASE / SULT1B1 / human cytosolic sulfotransferase / resveratrol / SGC / Cytoplasm / Lipid metabolism / Polymorphism / Steroid metabolism / Structural Genomics / Structural Genomics Consortium | ||||||
Function / homology | Function and homology information phenol-containing compound metabolic process / biogenic amine metabolic process / aryl sulfotransferase / thyroid hormone metabolic process / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process ...phenol-containing compound metabolic process / biogenic amine metabolic process / aryl sulfotransferase / thyroid hormone metabolic process / aryl sulfotransferase activity / Cytosolic sulfonation of small molecules / flavonoid metabolic process / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / epithelial cell differentiation / xenobiotic metabolic process / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Pan, P.W. / Tempel, W. / Dong, A. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. ...Pan, P.W. / Tempel, W. / Dong, A. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of human cytosolic sulfotransferase SULT1B1 in complex with PAP and resveratrol. Authors: Pan, P.W. / Tempel, W. / Dong, A. / Loppnau, P. / Kozieradzki, I. / Edwards, A.M. / Arrowsmith, C.H. / Weigelt, J. / Bountra, C. / Bochkarev, A. / Min, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ckl.cif.gz | 150 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ckl.ent.gz | 116 KB | Display | PDB format |
PDBx/mmJSON format | 3ckl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ck/3ckl ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3ckl | HTTPS FTP |
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-Related structure data
Related structure data | 1xv1 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
#1: Protein | Mass: 35093.324 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SULT1B1, ST1B2, SULT1B2 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) Strain (production host): BL21(DE3) codon plus RIL (Stratagene) References: UniProt: O43704, Transferases; Transferring sulfur-containing groups; Sulfotransferases #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: 2.47 Å3/Da / Density % sol: 50.23 % |
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 17% PEG 3350, 0.1M Ammonium sulfate, 0.001M DTT, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97926 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 28, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97926 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→50 Å / Num. all: 55786 / Num. obs: 55786 / % possible obs: 85.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 1.09 / Num. unique all: 1432 / Rsym value: 0.545 / % possible all: 22.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1XV1 1xv1 Resolution: 2→19.74 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.099 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.188 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Program coot 0.3.3 has also been used in refinement
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.293 Å2
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Refinement step | Cycle: LAST / Resolution: 2→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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