[English] 日本語
Yorodumi
- PDB-1j99: CRYSTAL STRUCTURE OF HUMAN DEHYDROEPIANDROSTERONE SULFOTRANSFERAS... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1j99
TitleCRYSTAL STRUCTURE OF HUMAN DEHYDROEPIANDROSTERONE SULFOTRANSFERASE IN COMPLEX WITH SUBSTRATE
ComponentsALCOHOL SULFOTRANSFERASE
KeywordsTRANSFERASE / Dehydroepiandosterone / Sulfotransferase / DHEA
Function / homology
Function and homology information


bile-salt sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / bile acid catabolic process / thyroid hormone metabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process ...bile-salt sulfotransferase / alcohol sulfotransferase activity / bile-salt sulfotransferase activity / alcohol sulfotransferase / steroid sulfotransferase activity / bile acid catabolic process / thyroid hormone metabolic process / 3'-phosphoadenosine 5'-phosphosulfate binding / Cytosolic sulfonation of small molecules / 3'-phosphoadenosine 5'-phosphosulfate metabolic process / sulfation / ethanol catabolic process / sulfotransferase activity / Paracetamol ADME / steroid metabolic process / lipid catabolic process / cholesterol metabolic process / xenobiotic metabolic process / PPARA activates gene expression / cytosol / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / MERCURY (II) IODIDE / IODIDE ION / Sulfotransferase 2A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsRehse, P.H. / Zhou, M. / Lin, S.-X.
CitationJournal: Biochem.J. / Year: 2002
Title: Crystal structure of human dehydroepiandrosterone sulphotransferase in complex with substrate.
Authors: Rehse, P.H. / Zhou, M. / Lin, S.X.
History
DepositionMay 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ALTHOUGH SOLUTION STUDIES INDICATE THAT DHEA-ST IS A DIMER IN SOLUTION, IT IS NOT CLEAR AS TO WHAT THE DIMER IS. THE AUTHOR DOES NOT WISH TO DEFINE THE DIMER.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALCOHOL SULFOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4956
Polymers34,7171
Non-polymers1,7795
Water3,891216
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.931, 137.976, 45.864
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein ALCOHOL SULFOTRANSFERASE / / DEHYDROEPIANDROSTERONE SULFOTRANSFERASE / DHEA-ST / HYDROXYSTEROID SULFOTRANSFERASE / HST


Mass: 34716.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q06520, alcohol sulfotransferase
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#3: Chemical ChemComp-HGI / MERCURY (II) IODIDE / MERCURY DIIODIDE / Mercury(II) iodide


Mass: 454.399 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HgI2
#4: Chemical ChemComp-AND / 3-BETA-HYDROXY-5-ANDROSTEN-17-ONE / Dehydroepiandrosterone


Mass: 288.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H28O2 / Comment: hormone*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 65.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris, cobalt chloride, amonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mMTris1reservoirpH7.5
21.2 mM1reservoirCoCl2
3170 mMammonium sulfate1reservoir
412 mg/mlDHEA-ST1drop0.35mM
50.5 mMDHEA1drop
610 mMTris1droppH7.5
70.5 mMEDTA1drop
80.1 %n-octyl-beta-D-glucopyranoside1drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.04 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 1999
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.99→40 Å / Num. all: 32427 / Num. obs: 32427 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.6
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3189 / % possible all: 93.5
Reflection
*PLUS
Lowest resolution: 40 Å / Num. obs: 32429 / Num. measured all: 116140 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 93.5 % / Rmerge(I) obs: 0.555 / Mean I/σ(I) obs: 3.1

-
Processing

Software
NameClassification
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQU

1aqu


Resolution: 1.99→38 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3112 -random
Rwork0.231 ---
all-31210 --
obs-34833 89.6 %-
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å2-4.58 Å22.29 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.99→38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2377 0 52 216 2645
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 1.99→2.11 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.329 450 -
Rwork0.312 --
obs-5689 84.3 %
Refinement
*PLUS
% reflection Rfree: 10 % / Rfactor obs: 0.231 / Rfactor Rfree: 0.262 / Rfactor Rwork: 0.231
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.13
LS refinement shell
*PLUS
Rfactor Rfree: 0.329 / Rfactor Rwork: 0.312 / Rfactor obs: 0.312

+
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