[English] 日本語
![](img/lk-miru.gif)
- PDB-1q1q: Crystal structure of human pregnenolone sulfotransferase (SULT2B1... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 1q1q | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human pregnenolone sulfotransferase (SULT2B1a) in the presence of PAP | ||||||
![]() | sulfotransferase family, cytosolic, 2B, member 1 isoform a | ||||||
![]() | TRANSFERASE / sulfotransferase / pregnenolone / SULT2B1 / PAP | ||||||
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 |
| ||||||
Remark 350 | BIOLOGICAL UNIT UNKNOWN |
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 71.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 51.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 829.9 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 844.4 KB | Display | |
Data in XML | ![]() | 14.7 KB | Display | |
Data in CIF | ![]() | 19 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1q1zC ![]() 1q20C ![]() 1q22C ![]() 1efhS C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | not known |
-
Components
#1: Protein | Mass: 39645.871 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
---|---|---|---|
#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-A3P / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.66 % | |||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.8M sodium tartrate, 0.2M Li2So4, 0.1M CHES, 4mM PAP, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 5, 2001 / Details: MSC Yale 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: 2.9→25 Å / Num. obs: 29928 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 80.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.9→3 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 2.1 / Num. unique all: 2991 / % possible all: 98.5 |
Reflection | *PLUS Lowest resolution: 25 Å / % possible obs: 99 % / Num. measured all: 105367 |
Reflection shell | *PLUS % possible obs: 98.5 % |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1EFH Resolution: 2.91→21.94 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
| ||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.3004 Å2 / ksol: 0.294595 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.3 Å2
| ||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.91→21.94 Å
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
| ||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Rfactor Rfree: 0.41 / Rfactor Rwork: 0.41 |