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- PDB-5mex: Sulphotransferase-18 from Arabidopsis thaliana in complex with 3'... -

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Basic information

Entry
Database: PDB / ID: 5mex
TitleSulphotransferase-18 from Arabidopsis thaliana in complex with 3'-phosphoadenosine 5'-phosphate (PAP)and sinigrin
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 / sulfation / 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
1,3-BUTANEDIOL / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / Sinigrin / Cytosolic sulfotransferase 18
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 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 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model / Author supporting evidence
Category: atom_site / pdbx_audit_support / pdbx_validate_close_contact
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp ...atom_site / chem_comp / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Jan 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cytosolic sulfotransferase 18
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,07714
Polymers37,5001
Non-polymers1,57713
Water5,152286
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint34 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.820, 63.820, 209.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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
#3: Sugar ChemComp-SZZ / Sinigrin


Type: D-saccharide / Mass: 359.373 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17NO9S2

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Non-polymers , 4 types, 298 molecules

#2: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

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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: 2.85 Å3/Da / Density % sol: 56.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 5.9
Details: 0.1 M 2-(N-morpholino) ethanesulfonic acid (MES) pH 5.9, 16% PEG4000, 160 mM NaCl, and 4% 1,3-butanediol

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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
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: 1.92→47.16 Å / Num. obs: 34239 / % possible obs: 99.7 % / Redundancy: 10.55 % / Biso Wilson estimate: 37.25 Å2 / Rmerge(I) obs: 0.0647 / Rsym value: 0.027 / Net I/σ(I): 22.68
Reflection shellResolution: 1.92→2.02 Å / Redundancy: 9.15 % / Rmerge(I) obs: 0.5435 / Mean I/σ(I) obs: 3.21 / % possible all: 98.3

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Processing

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

1q44


Resolution: 1.92→19.95 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.105 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.128 / ESU R Free: 0.13 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21701 1726 5.1 %RANDOM
Rwork0.16816 ---
obs0.17061 32384 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 33.268 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.92→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2647 0 95 286 3028
Refine LS restraintsType: r_sphericity_bonded
LS refinement shellResolution: 1.92→1.969 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 101 -
Rwork0.27 2278 -
obs--97.22 %

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