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- PDB-1q22: Crystal structure of human cholesterol sulfotransferase (SULT2B1b... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1q22 | ||||||
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Title | Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of DHEA and PAP | ||||||
![]() | sulfotransferase family, cytosolic, 2B, member 1 isoform b | ||||||
![]() | TRANSFERASE / sulfotransferase / dhea / PAP / SULT2B1b | ||||||
Function / homology | ![]() cholesterol sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfotransferase activity / steroid hormone binding / cholesterol binding / positive regulation of epidermal cell differentiation ...cholesterol sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / sulfotransferase activity / steroid hormone binding / cholesterol binding / positive regulation of epidermal cell differentiation / steroid metabolic process / small molecule binding / cholesterol metabolic process / nucleic acid binding / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / endoplasmic reticulum / extracellular exosome / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lee, K.A. / Fuda, H. / Lee, Y.C. / Negishi, M. / Strott, C.A. / Pedersen, L.C. | ||||||
![]() | ![]() Title: Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between ...Title: Crystal structure of human cholesterol sulfotransferase (SULT2B1b) in the presence of pregnenolone and 3'-phosphoadenosine 5'-phosphate. Rationale for specificity differences between prototypical SULT2A1 and the SULT2BG1 isoforms. Authors: Lee, K.A. / Fuda, H. / Lee, Y.C. / Negishi, M. / Strott, C.A. / Pedersen, L.C. | ||||||
History |
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Remark 350 | BIOLOGICAL UNIT UNKNOWN |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 75.8 KB | Display | ![]() |
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PDB format | ![]() | 54.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.1 KB | Display | |
Data in CIF | ![]() | 18.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q1qC ![]() 1q1zC ![]() 1q20SC C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Details | not known |
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Components
#1: Protein | Mass: 34157.012 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Chemical | ChemComp-NA / |
#3: Chemical | ChemComp-A3P / |
#4: Chemical | ChemComp-AND / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: sodium citrate and imidizole, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 10, 2003 / Details: MSC Blue mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. all: 25505 / Num. obs: 25505 / % possible obs: 96 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 44.7 Å2 / Rsym value: 0.119 / Net I/σ(I): 25.9 |
Reflection shell | Resolution: 2.5→2.59 Å / Redundancy: 4 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 2245 / Rsym value: 0.377 / % possible all: 86.8 |
Reflection | *PLUS % possible obs: 96 % / Num. measured all: 141095 / Rmerge(I) obs: 0.119 |
Reflection shell | *PLUS % possible obs: 86.8 % / Rmerge(I) obs: 0.377 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: SULT2B1b with PAP and pregnenolone bound, PDB entry 1Q20 Resolution: 2.5→48.67 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.02 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 30.4903 Å2 / ksol: 0.31634 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.5→48.67 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Highest resolution: 2.5 Å | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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