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- PDB-6ktv: The structure of EanB complex with hercynine and persulfided Cys412 -

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Basic information

Entry
Database: PDB / ID: 6ktv
TitleThe structure of EanB complex with hercynine and persulfided Cys412
ComponentsSulfurtransferase
KeywordsTRANSFERASE / complex / persulfide
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
N,N,N-trimethyl-histidine / IMIDAZOLE / NICKEL (II) ION / 1,3-PROPANDIOL / DI(HYDROXYETHYL)ETHER / Sulfurtransferase
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,52634
Polymers52,2661
Non-polymers2,26033
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-47 kcal/mol
Surface area18070 Å2
Unit cell
Length a, b, c (Å)88.675, 112.819, 60.615
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfurtransferase


Mass: 52266.203 Da / Num. of mol.: 1
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 , 11 types, 265 molecules

#2: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2
#10: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#11: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES/imidazole pH6.5, 0.02M of each alcohol, 10%PEG20k, 20%PEG550MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 31581 / % possible obs: 99.8 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 12.9
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 1.041 / Num. unique obs: 1530

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
PHENIX1.12refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KTX

6ktx


Resolution: 2.2→45.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.1991 1491 4.96 %
Rwork0.17 --
obs0.1715 30079 94.88 %
Refinement stepCycle: LAST / Resolution: 2.2→45.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3459 0 136 232 3827
LS refinement shellResolution: 2.198→2.269 Å /
Rfactor% reflection
Rfree0.2985 -
Rwork0.2153 -
obs-70 %

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