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- PDB-8eg3: Structure of human placental steroid (estrone/DHEA) sulfatase at ... -

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Basic information

Entry
Database: PDB / ID: 8eg3
TitleStructure of human placental steroid (estrone/DHEA) sulfatase at 2.0 angstrom resolution
ComponentsSteryl-sulfataseSteroid sulfatase
KeywordsHYDROLASE / Steroid / sulfatase / sex steroid biosynthesis / ER membrane-bound enzyme
Function / homology
Function and homology information


steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / Glycosphingolipid catabolism / steroid catabolic process / epidermis development / female pregnancy ...steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / Glycosphingolipid catabolism / steroid catabolic process / 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
C-terminal region of aryl-sulfatase / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / Steryl-sulfatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.04 Å
AuthorsGhosh, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)62794 United States
CitationJournal: 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
DepositionSep 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Steryl-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8097
Polymers65,6471
Non-polymers1,1626
Water2,396133
1
A: Steryl-sulfatase
hetero molecules

A: Steryl-sulfatase
hetero molecules

A: Steryl-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,42821
Polymers196,9413
Non-polymers3,48718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11910 Å2
ΔGint-58 kcal/mol
Surface area63230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.190, 117.190, 102.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-603-

PO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Steryl-sulfatase / Steroid sulfatase / Arylsulfatase C / ASC / Estrone sulfatase / Steroid sulfatase / Steryl-sulfate sulfohydrolase


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 ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 3 types, 135 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: MPD, ammonium phosphate, BOG, Tris buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1P49

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
RfactorNum. reflection% reflection
Rfree0.2505 2535 4.95 %
Rwork0.2195 48728 -
obs0.2211 51263 98.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.29 Å2 / Biso mean: 67.9822 Å2 / Biso min: 27.31 Å2
Refinement stepCycle: final / Resolution: 2.04→32.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4369 0 74 133 4576
Biso mean--61.14 51.18 -
Num. residues----554
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.080.38191470.344426942841100
2.08-2.130.29281320.296327202852100
2.13-2.170.29331250.284127052830100
2.17-2.220.29931270.2727182845100
2.22-2.280.31371660.293626742840100
2.28-2.340.2911380.255227202858100
2.34-2.410.24771180.245727232841100
2.41-2.490.30011450.248127162861100
2.49-2.580.27581420.249227192861100
2.58-2.680.26811620.240227132875100
2.68-2.80.27451470.232727002847100
2.8-2.950.26171620.235127392901100
2.95-3.130.26541530.240127042857100
3.13-3.370.23971300.217727702900100
3.37-3.710.2291650.202727392904100
3.71-4.250.20791180.167927842902100
4.25-5.350.18061360.17552777291399
5.35-32.130.28821220.22992413253583
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.71041.9272-0.88553.7973-1.96983.6597-0.22310.0309-0.0256-0.9247-0.0152-0.18950.28620.36830.17520.56730.06820.04670.22580.01030.240268.70225.775426.9756
22.7285-2.79861.23394.8827-1.19712.01060.1462-0.05720.1971-0.7441-0.0896-0.261-0.00080.0782-0.01560.36020.02760.04040.17560.01530.272568.1113-28.78643.0578
33.05591.5602-1.23634.0449-2.94214.0815-0.5570.4271-0.0444-1.90590.2263-0.14831.13990.23060.09141.1070.03930.12770.2816-0.05720.217867.63913.331617.0453
41.67751.1648-0.66064.3324-2.1254.4841-0.0501-0.3013-0.3879-0.7904-0.8624-1.47060.39241.80650.26660.36410.24560.28660.95910.31670.710984.0553.500830.7925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 23 through 170 )A23 - 170
2X-RAY DIFFRACTION2chain 'A' and (resid 171 through 241 )A171 - 241
3X-RAY DIFFRACTION3chain 'A' and (resid 242 through 411 )A242 - 411
4X-RAY DIFFRACTION4chain 'A' and (resid 412 through 576 )A412 - 576

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