[English] 日本語
Yorodumi
- PDB-5mek: Sulphotransferase-18 from Arabidopsis thaliana in complex with 3'... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mek
TitleSulphotransferase-18 from Arabidopsis thaliana in complex with 3'-phosphoadenosine 5'-phosphate (PAP)
ComponentsCytosolic sulfotransferase 18
KeywordsTRANSFERASE / Sulphotransferases / glucosinolate-biosynthesis / catalysis
Function / homology
Function and homology information


aliphatic desulfoglucosinolate sulfotransferase / aliphatic desulfoglucosinolate sulfotransferase activity / glucosinolate biosynthetic process / aromatic desulfoglucosinolate sulfotransferase activity / cytoplasm
Similarity search - Function
Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / N-PROPANOL / Cytosolic sulfotransferase 18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsHirschmann, F. / Krause, F. / Baruch, P. / Chizhov, I. / Mueller, J.W. / Manstein, D.J. / Papenbrock, J. / Fedorov, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationPA 764/10-1 Germany
German Research FoundationFE 1510/2-1 Germany
CitationJournal: Sci Rep / Year: 2017
Title: Structural and biochemical studies of sulphotransferase 18 from Arabidopsis thaliana explain its substrate specificity and reaction mechanism.
Authors: Hirschmann, F. / Krause, F. / Baruch, P. / Chizhov, I. / Mueller, J.W. / Manstein, D.J. / Papenbrock, J. / Fedorov, R.
History
DepositionNov 15, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cytosolic sulfotransferase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,59329
Polymers37,5001
Non-polymers2,09328
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint77 kcal/mol
Surface area14140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.740, 62.740, 201.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

-
Components

#1: Protein Cytosolic sulfotransferase 18 / AtSOT18 / Desulfo-glucosinolate sulfotransferase B / Sulfotransferase 5B / AtST5b


Mass: 37499.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: SOT18, ST5B, At1g74090, F2P9.4 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9C9C9, Transferases; Transferring sulfur-containing groups; Sulfotransferases
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-POL / N-PROPANOL / 1-PROPONOL


Mass: 60.095 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.64 Å3/Da / Density % sol: 53.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.9
Details: 0.1 M MES pH 5.9, 16.5% PEG4000, 160 mM NaCl and 5% 1-propanol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 12, 2014
Details: Pt coated mirrors in a Kirkpatrick-Baez geometry as the focusing system
RadiationMonochromator: horizontally diffracting Si (111) monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.74→45.85 Å / Num. obs: 42500 / % possible obs: 100 % / Redundancy: 21.66 % / Biso Wilson estimate: 32.7 Å2 / Rmerge(I) obs: 0.0927 / Rsym value: 0.0275 / Net I/σ(I): 20.44
Reflection shellResolution: 1.74→1.84 Å / Redundancy: 22.33 % / Rmerge(I) obs: 0.7532 / Mean I/σ(I) obs: 2.65 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SADABSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-ID: 1Q44

1q44


Resolution: 1.74→19.99 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.203 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.102 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20755 2137 5 %RANDOM
Rwork0.16745 ---
obs0.16946 40227 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.185 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: 1 / Resolution: 1.74→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 135 242 3024
Refine LS restraintsType: r_scangle_other / Dev ideal: 5.666 / Dev ideal target: 4.366 / Number: 2217
LS refinement shellResolution: 1.74→1.785 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 158 -
Rwork0.262 2878 -
obs--100 %

+
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