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- PDB-6h99: Crystal structure of anaerobic ergothioneine biosynthesis enzyme ... -

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Basic information

Entry
Database: PDB / ID: 6h99
TitleCrystal structure of anaerobic ergothioneine biosynthesis enzyme from Chlorobium limicola in persulfide form.
ComponentsSulfurtransferase
KeywordsTRANSFERASE / metabolic role: anaerobic ergothioneine biosynthesis chemical activity: sulfur transfer / C-S bond formation protein family: rhodanese-like enzyme (PF00581)
Function / homology
Function and homology information


thiosulfate sulfurtransferase activity
Similarity search - Function
Rhodanese C-terminal signature. / Thiosulphate sulfurtransferase, conserved site / Rhodanese-like domain / Oxidized Rhodanese; domain 1 / Rhodanese Homology Domain / Rhodanese-like domain / Rhodanese domain profile. / Rhodanese-like domain superfamily / Rhodanese-like domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Sulfurtransferase
Similarity search - Component
Biological speciesChlorobium limicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLeisinger, F. / Burn, R. / Meury, M. / Lukat, P. / Seebeck, F.P.
Funding support Switzerland, 2items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
European Research CouncilERC-2013- StG 336559 Switzerland
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Structural and Mechanistic Basis for Anaerobic Ergothioneine Biosynthesis.
Authors: Leisinger, F. / Burn, R. / Meury, M. / Lukat, P. / Seebeck, F.P.
History
DepositionAug 3, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sulfurtransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55812
Polymers50,0591
Non-polymers49911
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-67 kcal/mol
Surface area17710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.760, 43.183, 88.740
Angle α, β, γ (deg.)90.00, 108.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

21A-762-

HOH

31A-1077-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfurtransferase /


Mass: 50058.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Persulfide-cysteine (CSS) in active site / Source: (gene. exp.) Chlorobium limicola (bacteria) / Strain: DSM 245 / NBRC 103803 / 6330 / Gene: Clim_1149 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): B / References: UniProt: B3ECE3

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Non-polymers , 6 types, 521 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 8000, magnesium chloride, Tris buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→43.542 Å / Num. obs: 61965 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.992 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.038 / Rrim(I) all: 0.099 / Net I/σ(I): 11.3
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.6331 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3057 / CC1/2: 0.82 / Rpim(I) all: 0.279 / Rrim(I) all: 0.706 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure

Resolution: 1.6→43.542 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.77
RfactorNum. reflection% reflection
Rfree0.1946 3118 5.03 %
Rwork0.1627 --
obs0.1643 61927 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→43.542 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3385 0 25 510 3920
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013531
X-RAY DIFFRACTIONf_angle_d1.0324806
X-RAY DIFFRACTIONf_dihedral_angle_d5.7983594
X-RAY DIFFRACTIONf_chiral_restr0.068489
X-RAY DIFFRACTIONf_plane_restr0.008634
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.6250.24131650.19922635X-RAY DIFFRACTION100
1.625-1.65170.25581510.19172645X-RAY DIFFRACTION100
1.6517-1.68020.24471360.19542629X-RAY DIFFRACTION100
1.6802-1.71070.23361410.18582685X-RAY DIFFRACTION100
1.7107-1.74360.25791210.19212654X-RAY DIFFRACTION100
1.7436-1.77920.22391310.19472652X-RAY DIFFRACTION100
1.7792-1.81790.2081290.18922671X-RAY DIFFRACTION100
1.8179-1.86020.23751340.1822676X-RAY DIFFRACTION100
1.8602-1.90670.22591320.18312675X-RAY DIFFRACTION100
1.9067-1.95830.25251530.18842661X-RAY DIFFRACTION100
1.9583-2.01590.22521370.17072640X-RAY DIFFRACTION100
2.0159-2.08090.20051380.17352650X-RAY DIFFRACTION100
2.0809-2.15530.18521370.16472682X-RAY DIFFRACTION100
2.1553-2.24160.19081410.16722682X-RAY DIFFRACTION100
2.2416-2.34360.21411510.17282643X-RAY DIFFRACTION100
2.3436-2.46720.22481340.16672677X-RAY DIFFRACTION100
2.4672-2.62170.2061430.16262708X-RAY DIFFRACTION100
2.6217-2.82410.22381330.16382667X-RAY DIFFRACTION100
2.8241-3.10830.19671540.16032681X-RAY DIFFRACTION100
3.1083-3.55780.16891500.1522688X-RAY DIFFRACTION100
3.5578-4.48180.15691460.13432716X-RAY DIFFRACTION100
4.4818-43.55770.141610.1382792X-RAY DIFFRACTION100

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