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

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Basic information

Entry
Database: PDB / ID: 8qfp
TitleErgothioneine dioxygenase from Thermocatellispora tengchongensis in complex with manganese and in presence of catalase anaerobic
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 / : / Cysteine dioxygenase
Function and homology information
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: 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
Revision 1.2Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,8078
Polymers41,4082
Non-polymers3996
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.654, 59.198, 134.103
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, 95 molecules

#2: 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
#3: 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
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 42.53 %
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: Dec 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→44.38 Å / Num. obs: 37187 / % possible obs: 99.3 % / Redundancy: 2 % / CC1/2: 0.998 / CC star: 0.999 / Net I/σ(I): 10.22
Reflection shellResolution: 2.2→2.279 Å / Mean I/σ(I) obs: 2.05 / Num. unique obs: 3677 / CC1/2: 0.97

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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: 2.2→44.38 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2646 1720 4.97 %
Rwork0.2115 --
obs0.2141 34599 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 18 89 2559
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052528
X-RAY DIFFRACTIONf_angle_d0.7463433
X-RAY DIFFRACTIONf_dihedral_angle_d6.955352
X-RAY DIFFRACTIONf_chiral_restr0.05352
X-RAY DIFFRACTIONf_plane_restr0.004454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.42681420.31532769X-RAY DIFFRACTION100
2.26-2.340.29411410.28842744X-RAY DIFFRACTION100
2.34-2.420.31941330.25582728X-RAY DIFFRACTION99
2.42-2.520.34681220.25622784X-RAY DIFFRACTION100
2.52-2.630.31370.24832681X-RAY DIFFRACTION96
2.63-2.770.25481640.2132707X-RAY DIFFRACTION99
2.77-2.950.24471560.21562754X-RAY DIFFRACTION100
2.95-3.170.2651570.20092739X-RAY DIFFRACTION100
3.17-3.490.26341460.19752764X-RAY DIFFRACTION100
3.49-40.2491320.18942750X-RAY DIFFRACTION99
4-5.030.23671470.17312702X-RAY DIFFRACTION98
5.03-44.380.24311430.20462757X-RAY DIFFRACTION100

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