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

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Basic information

Entry
Database: PDB / ID: 8qfr
TitleErgothioneine dioxygenase from Thermocatellispora tengchongensis in complex with nickel and substrate (anaerobic)
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
ACETATE ION / Chem-LW8 / NICKEL (II) ION / Cysteine dioxygenase
Similarity search - Component
Biological speciesThermocatellispora tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVasseur, C.M. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182023 Switzerland
CitationJournal: To Be Published
Title: Ergothioneine dioxygenase from Thermocatellispora tengchongensis in complex with nickel and substrate (anaerobic)
Authors: Nalivaiko, E. / Vasseur, C.M. / Seebeck, F.P.
History
DepositionSep 4, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

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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)41,63313
Polymers40,7632
Non-polymers87011
Water2,720151
1
A: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7976
Polymers20,3821
Non-polymers4155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Cysteine dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8367
Polymers20,3821
Non-polymers4546
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.633, 59.088, 134.446
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: 20381.537 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TEV cleavage during purification process
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 , 8 types, 162 molecules

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


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: 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.: 1 / Source method: obtained synthetically / Formula: C9H16N3O2S / 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#8: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.71 Å3/Da / Density % sol: 54.67 %
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: Jun 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42.36 Å / Num. obs: 37404 / % possible obs: 99.77 % / Redundancy: 2 % / CC1/2: 0.998 / Net I/σ(I): 10.8
Reflection shellResolution: 2.2→2.279 Å / Num. unique obs: 3652 / CC1/2: 0.973

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→42.36 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1727 4.97 %
Rwork0.1793 --
obs0.1814 34770 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 46 151 2501
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012402
X-RAY DIFFRACTIONf_angle_d1.1913258
X-RAY DIFFRACTIONf_dihedral_angle_d8.576341
X-RAY DIFFRACTIONf_chiral_restr0.073340
X-RAY DIFFRACTIONf_plane_restr0.007432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.22071220.20252774X-RAY DIFFRACTION99
2.26-2.340.24781200.19132783X-RAY DIFFRACTION100
2.34-2.420.1951660.17812685X-RAY DIFFRACTION99
2.42-2.520.29211420.18682756X-RAY DIFFRACTION99
2.52-2.630.26891120.18452833X-RAY DIFFRACTION100
2.63-2.770.2151560.17832712X-RAY DIFFRACTION100
2.77-2.950.21241340.18332783X-RAY DIFFRACTION100
2.95-3.170.25011730.18652718X-RAY DIFFRACTION100
3.17-3.490.18741560.18742758X-RAY DIFFRACTION99
3.49-40.19711670.15952720X-RAY DIFFRACTION100
4-5.030.25321390.16092761X-RAY DIFFRACTION100
5.04-42.360.19231400.18992760X-RAY DIFFRACTION100

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