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Yorodumi- PDB-8eg3: Structure of human placental steroid (estrone/DHEA) sulfatase at ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8eg3 | ||||||
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Title | Structure of human placental steroid (estrone/DHEA) sulfatase at 2.0 angstrom resolution | ||||||
Components | Steryl-sulfatase | ||||||
Keywords | HYDROLASE / Steroid / sulfatase / sex steroid biosynthesis / ER membrane-bound enzyme | ||||||
Function / homology | Function and homology information steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / microneme membrane / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / steroid catabolic process / Glycosphingolipid catabolism / epidermis development ...steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / microneme membrane / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / steroid catabolic process / Glycosphingolipid catabolism / epidermis development / female pregnancy / lysosome / endosome / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 Å | ||||||
Authors | Ghosh, D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Steroid Biochem.Mol.Biol. / Year: 2022 Title: Structure of human placental steroid sulfatase at 2.0 angstrom resolution: Catalysis, quaternary association, and a secondary ligand site. Authors: Ghosh, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8eg3.cif.gz | 243.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8eg3.ent.gz | 194.3 KB | Display | PDB format |
PDBx/mmJSON format | 8eg3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8eg3_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8eg3_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8eg3_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 8eg3_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/eg/8eg3 ftp://data.pdbj.org/pub/pdb/validation_reports/eg/8eg3 | HTTPS FTP |
-Related structure data
Related structure data | 1p49S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 65647.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P08842, steryl-sulfatase |
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-Sugars , 2 types, 4 molecules
#3: Sugar | #5: Sugar | |
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-Non-polymers , 3 types, 135 molecules
#2: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-PO4 / |
#6: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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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: 3.1 Å3/Da / Density % sol: 60.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: MPD, ammonium phosphate, BOG, Tris buffer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.04→72.18 Å / Num. obs: 51319 / % possible obs: 99 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.04→2.15 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7486 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1P49 Resolution: 2.04→32.13 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.95 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.29 Å2 / Biso mean: 67.9822 Å2 / Biso min: 27.31 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.04→32.13 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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