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- PDB-6kw0: The structure of EanB/Y353F-Cys412-persulfide in tetrahedral inte... -

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Basic information

Entry
Database: PDB / ID: 6kw0
TitleThe structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with ergothioneine
ComponentsSulfurtransferase
KeywordsTRANSFERASE / intermediate / mutant / ergothioneine
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-LW8 / TRIETHYLENE GLYCOL / Sulfurtransferase
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsWu, L. / Liu, P.H. / Zhou, J.H.
CitationJournal: To Be Published
Title: The structure of EanB/Y353F-Cys412-persulfide in tetrahedral intermediate state with ergothioneine
Authors: Wu, L. / Liu, P.H. / Zhou, J.H.
History
DepositionSep 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 9, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 20, 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
B: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,36212
Polymers104,4362
Non-polymers92610
Water21612
1
A: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7386
Polymers52,2181
Non-polymers5205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area17870 Å2
MethodPISA
2
B: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6246
Polymers52,2181
Non-polymers4055
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-12 kcal/mol
Surface area17780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.206, 87.413, 92.106
Angle α, β, γ (deg.)90.000, 91.800, 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 AB

#1: Protein Sulfurtransferase


Mass: 52218.137 Da / Num. of mol.: 2 / Mutation: Y353F
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 , 6 types, 22 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-LW8 / trimethyl-[(2S)-1-oxidanyl-1-oxidanylidene-3-(2-sulfanylidene-1,3-dihydroimidazol-4-yl)propan-2-yl]azanium


Mass: 230.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O2S / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES/imidazole pH6.5 0.03 M of each halide 12.5% PEG1000 12.5%PEG3350 12.5% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 23952 / % possible obs: 99.8 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.245 / Net I/σ(I): 8.7
Reflection shellResolution: 2.79→2.84 Å / Rmerge(I) obs: 1.614 / Num. unique obs: 1182

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→49 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2504 1083 4.99 %
Rwork0.196 --
obs0.1988 21706 89 %
Refinement stepCycle: LAST / Resolution: 2.8→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6784 0 47 12 6843

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