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Yorodumi- PDB-1q1q: Crystal structure of human pregnenolone sulfotransferase (SULT2B1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q1q | ||||||
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Title | Crystal structure of human pregnenolone sulfotransferase (SULT2B1a) in the presence of PAP | ||||||
Components | sulfotransferase family, cytosolic, 2B, member 1 isoform a | ||||||
Keywords | TRANSFERASE / sulfotransferase / pregnenolone / SULT2B1 / PAP | ||||||
Function / homology | Function and homology information 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 / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.91 Å | ||||||
Authors | Lee, K.A. / Fuda, H. / Lee, Y.C. / Negishi, M. / Strott, C.A. / Pedersen, L.C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 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 |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q1q.cif.gz | 71.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q1q.ent.gz | 51.3 KB | Display | PDB format |
PDBx/mmJSON format | 1q1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/1q1q ftp://data.pdbj.org/pub/pdb/validation_reports/q1/1q1q | HTTPS FTP |
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-Related structure data
Related structure data | 1q1zC 1q20C 1q22C 1efhS C: citing same article (ref.) 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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Unit cell |
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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.) Homo sapiens (human) / Gene: SULT2B1 / Plasmid: PGEX-6P-3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: O00204 | ||
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#2: Chemical | ChemComp-NA / | ||
#3: Chemical | ChemComp-A3P / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.5 Å3/Da / Density % sol: 72.66 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å |
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 |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 15.3004 Å2 / ksol: 0.294595 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.91→21.94 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
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Xplor file |
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Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.41 / Rfactor Rwork: 0.41 |