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

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8qfm
TitleErgothioneine dioxygenase from Thermocatellispora tengchongensis in complex with manganese
ComponentsCysteine dioxygenase
KeywordsOXIDOREDUCTASE / thiol dioxygenase Ergothioneine Dioxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / ferrous iron binding
Similarity search - Function
Cysteine dioxygenase type I / Cysteine dioxygenase type I / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / HYDROGEN PEROXIDE / Cysteine dioxygenase
Similarity search - Component
Biological speciesThermocatellispora tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)42,36917
Polymers41,4082
Non-polymers96115
Water3,117173
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-10 kcal/mol
Surface area14220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.531, 59.240, 133.986
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 , 7 types, 188 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.13 Å3/Da / Density % sol: 42.36 %
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: Aug 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→44.38 Å / Num. obs: 57347 / % possible obs: 99.74 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 14.51
Reflection shellResolution: 1.9→1.968 Å / Mean I/σ(I) obs: 1.96 / Num. unique obs: 5521 / CC1/2: 0.793

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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: 1.9→44.38 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2165 2675 4.97 %
Rwork0.1845 --
obs0.1861 53834 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 56 173 2586
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062469
X-RAY DIFFRACTIONf_angle_d0.933333
X-RAY DIFFRACTIONf_dihedral_angle_d22.771350
X-RAY DIFFRACTIONf_chiral_restr0.052346
X-RAY DIFFRACTIONf_plane_restr0.004434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.930.31411260.29522663X-RAY DIFFRACTION98
1.93-1.970.31691620.27092635X-RAY DIFFRACTION99
1.97-2.010.32691210.24172729X-RAY DIFFRACTION100
2.01-2.060.28451650.23192668X-RAY DIFFRACTION100
2.06-2.10.24921560.21282678X-RAY DIFFRACTION100
2.1-2.160.2431230.19422698X-RAY DIFFRACTION100
2.16-2.210.20621240.19462718X-RAY DIFFRACTION100
2.21-2.280.22431440.18922715X-RAY DIFFRACTION100
2.28-2.350.23481440.17982696X-RAY DIFFRACTION100
2.35-2.440.2181230.16892706X-RAY DIFFRACTION100
2.44-2.530.21941280.18252693X-RAY DIFFRACTION100
2.53-2.650.20791800.16932675X-RAY DIFFRACTION100
2.65-2.790.20391340.16992718X-RAY DIFFRACTION100
2.79-2.960.20771350.17612715X-RAY DIFFRACTION100
2.96-3.190.26541200.17712707X-RAY DIFFRACTION100
3.19-3.510.16641430.17642666X-RAY DIFFRACTION100
3.51-4.020.20641700.15922681X-RAY DIFFRACTION100
4.02-5.070.17131300.15472708X-RAY DIFFRACTION100
5.07-44.380.21911470.21072690X-RAY DIFFRACTION100

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