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- PDB-8qfl: Ergothioneine dioxygenase from Thermocatellispora tengchongensis ... -

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Basic information

Entry
Database: PDB / ID: 8qfl
TitleErgothioneine dioxygenase from Thermocatellispora tengchongensis in complex with iron
ComponentsCysteine dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase Ergothioneine Dioxygenase
Function / homologyCysteine dioxygenase type I / Cysteine dioxygenase type I / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold / ferrous iron binding / ACETATE ION / : / Cysteine dioxygenase
Function and homology information
Biological speciesThermocatellispora tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsVasseur, C.M. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182023 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Enzyme-Catalyzed Oxidative Degradation of Ergothioneine.
Authors: Nalivaiko, E.Y. / Vasseur, C.M. / Seebeck, F.P.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 27, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.year ..._citation.journal_volume / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine dioxygenase
B: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8568
Polymers41,4082
Non-polymers4486
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-41 kcal/mol
Surface area13640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.611, 58.946, 134.776
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cysteine dioxygenase


Mass: 20704.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermocatellispora tengchongensis (bacteria)
Gene: HNP84_002159 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A840P3H4

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Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium acetate tetrahydrate 0.1 M sodium cacodylate, pH 6.5 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→44.37 Å / Num. obs: 73060 / % possible obs: 99.53 % / Redundancy: 2 % / CC1/2: 0.9991 / CC star: 1 / Rmerge(I) obs: 0.01922 / Rpim(I) all: 0.01922 / Rrim(I) all: 0.02719 / Net I/σ(I): 17.69
Reflection shellResolution: 1.75→1.813 Å / Rmerge(I) obs: 0.2527 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 7074 / CC1/2: 0.884 / CC star: 0.969 / Rpim(I) all: 0.2527 / Rrim(I) all: 0.3573

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→44.37 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2124 3426 4.97 %
Rwork0.1727 --
obs0.1746 68925 99.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.75→44.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 24 164 2590
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0182509
X-RAY DIFFRACTIONf_angle_d1.3733404
X-RAY DIFFRACTIONf_dihedral_angle_d28.044349
X-RAY DIFFRACTIONf_chiral_restr0.096350
X-RAY DIFFRACTIONf_plane_restr0.011449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.29861600.30432681X-RAY DIFFRACTION98
1.78-1.80.391190.27882732X-RAY DIFFRACTION99
1.8-1.830.29171420.2442715X-RAY DIFFRACTION100
1.83-1.860.27941590.23912761X-RAY DIFFRACTION100
1.86-1.890.25231480.22092705X-RAY DIFFRACTION100
1.89-1.930.29051350.19562744X-RAY DIFFRACTION100
1.93-1.960.18441350.17522745X-RAY DIFFRACTION100
1.96-20.19791150.17022756X-RAY DIFFRACTION100
2-2.050.19011500.16392727X-RAY DIFFRACTION100
2.05-2.090.19631410.16612711X-RAY DIFFRACTION100
2.09-2.150.20661510.18012731X-RAY DIFFRACTION100
2.15-2.20.22541330.17892755X-RAY DIFFRACTION100
2.2-2.270.21961400.1812722X-RAY DIFFRACTION100
2.27-2.340.22251450.16932754X-RAY DIFFRACTION100
2.34-2.430.23311570.17662705X-RAY DIFFRACTION100
2.43-2.520.21191400.16352759X-RAY DIFFRACTION100
2.52-2.640.21481410.17042765X-RAY DIFFRACTION100
2.64-2.780.19091540.15982708X-RAY DIFFRACTION100
2.78-2.950.22951390.1722751X-RAY DIFFRACTION100
2.95-3.180.20651590.16812703X-RAY DIFFRACTION100
3.18-3.50.20841490.17122725X-RAY DIFFRACTION99
3.5-40.20591210.15092722X-RAY DIFFRACTION100
4.01-5.050.15611330.14552751X-RAY DIFFRACTION100
5.05-44.370.23031600.19132671X-RAY DIFFRACTION98

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