[English] 日本語
Yorodumi
- PDB-8eg3: Structure of human placental steroid (estrone/DHEA) sulfatase at ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8eg3
TitleStructure of human placental steroid (estrone/DHEA) sulfatase at 2.0 angstrom resolution
ComponentsSteryl-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 / sulfuric ester hydrolase activity / arylsulfatase activity / steroid catabolic process / Glycosphingolipid catabolism / epidermis development / female pregnancy ...steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / The activation of arylsulfatases / sulfuric ester hydrolase activity / arylsulfatase activity / steroid catabolic process / Glycosphingolipid catabolism / epidermis development / female pregnancy / lysosome / endosome / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / endoplasmic reticulum / Golgi apparatus / metal ion binding / membrane / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Steryl-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

-
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


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


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

-
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


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


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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more