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- PDB-6ku2: The structure of EanB/Y353A complex with ergothioneine covalent l... -

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Basic information

Entry
Database: PDB / ID: 6ku2
TitleThe structure of EanB/Y353A complex with ergothioneine covalent linked with persulfide Cys412
ComponentsSulfurtransferase
KeywordsTRANSFERASE / double mutant / hercynine / complex
Function / homology
Function and homology information


thiosulfate-cyanide sulfurtransferase activity / metal ion binding
Similarity search - Function
: / Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain
Similarity search - Domain/homology
BROMIDE ION / Chem-DV6 / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Sulfurtransferase
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsWu, L. / Liu, P.H. / Zhou, J.H.
CitationJournal: Acs Catalysis / Year: 2020
Title: Single-Step Replacement of an Unreactive C-H Bond by a C-S Bond Using Polysulfide as the Direct Sulfur Source in the Anaerobic Ergothioneine Biosynthesis
Authors: Cheng, R. / Wu, L. / Lai, R. / Peng, C. / Naowarojna, N. / Hu, W. / Li, X. / Whelan, S.A. / Lee, N. / Lopez, J. / Zhao, C. / Yong, Y. / Xue, J. / Jiang, X. / Grinstaff, M.W. / Deng, Z. / ...Authors: Cheng, R. / Wu, L. / Lai, R. / Peng, C. / Naowarojna, N. / Hu, W. / Li, X. / Whelan, S.A. / Lee, N. / Lopez, J. / Zhao, C. / Yong, Y. / Xue, J. / Jiang, X. / Grinstaff, M.W. / Deng, Z. / Chen, J. / Cui, Q. / Zhou, J.H. / Liu, P.
History
DepositionAug 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfurtransferase
E: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,71919
Polymers104,2842
Non-polymers1,43517
Water5,549308
1
A: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,8799
Polymers52,1421
Non-polymers7378
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-51 kcal/mol
Surface area17710 Å2
MethodPISA
2
E: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,84010
Polymers52,1421
Non-polymers6989
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-52 kcal/mol
Surface area17970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.683, 88.240, 90.771
Angle α, β, γ (deg.)90.000, 90.350, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AE

#1: Protein Sulfurtransferase


Mass: 52142.043 Da / Num. of mol.: 2 / Mutation: Y353A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium limicola (bacteria) / Strain: DSM 245 / NBRC 103803 / 6330 / Gene: Clim_1149 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: B3ECE3

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Non-polymers , 10 types, 325 molecules

#2: Chemical ChemComp-DV6 / [(2S)-3-[(2S)-2-(disulfanyl)-2,3-dihydro-1H-imidazol-4-yl]-1-oxidanyl-1-oxidanylidene-propan-2-yl]-trimethyl-azanium


Mass: 264.388 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H18N3O2S2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#7: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#8: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M imidazole, Sodium cacodylate, MES, Bis-tris pH6.5, 0.09M halogens (NaF,NaBr,NaI), 37.5% MPD_P1k_PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 41635 / % possible obs: 99.5 % / Redundancy: 6.7 % / CC1/2: 0.139 / Net I/σ(I): 14.7
Reflection shellResolution: 2.34→2.38 Å / Rmerge(I) obs: 0.896 / Num. unique obs: 2048

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Processing

Software
NameVersionClassification
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIX1.12-2829refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→47.34 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.22808 1890 4.8 %
Rwork0.17079 --
obs0.17351 37443 93.99 %
Refinement stepCycle: LAST / Resolution: 2.34→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6828 0 72 308 7208

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