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- PDB-8qfo: Ergothioneine dioxygenase, variant Y149F, from Thermocatellispora... -

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Basic information

Entry
Database: PDB / ID: 8qfo
TitleErgothioneine dioxygenase, variant Y149F, 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
ACETATE ION / : / DI(HYDROXYETHYL)ETHER / Cysteine dioxygenase
Similarity search - Component
Biological speciesThermocatellispora tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 1.1Jan 10, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Feb 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 1.3Mar 27, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,7939
Polymers41,3762
Non-polymers4177
Water84747
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)44.684, 59.667, 134.611
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: 20688.025 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, 54 molecules

#2: 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
#3: 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
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2 / 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.: 47 / 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: 2.17 Å3/Da / Density % sol: 43.28 %
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: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→44.65 Å / Num. obs: 46424 / % possible obs: 99.28 % / Redundancy: 2 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.01988 / Rrim(I) all: 0.02812 / Net I/σ(I): 12.86
Reflection shellResolution: 2.05→2.123 Å / Mean I/σ(I) obs: 2.51 / Num. unique obs: 4565 / CC1/2: 0.936

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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: 2.05→44.65 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2614 2223 5.13 %
Rwork0.2132 --
obs0.2156 43345 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→44.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2455 0 22 47 2524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032540
X-RAY DIFFRACTIONf_angle_d0.6033446
X-RAY DIFFRACTIONf_dihedral_angle_d17.854346
X-RAY DIFFRACTIONf_chiral_restr0.046353
X-RAY DIFFRACTIONf_plane_restr0.003459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.090.40831490.34982544X-RAY DIFFRACTION99
2.09-2.140.35221300.32682577X-RAY DIFFRACTION99
2.14-2.20.36781220.30662613X-RAY DIFFRACTION100
2.2-2.260.46921660.36642532X-RAY DIFFRACTION99
2.26-2.320.31411260.28382567X-RAY DIFFRACTION99
2.32-2.40.30271400.25392588X-RAY DIFFRACTION100
2.4-2.480.27671520.23342593X-RAY DIFFRACTION99
2.48-2.580.26691240.23822535X-RAY DIFFRACTION99
2.58-2.70.29851440.23062543X-RAY DIFFRACTION99
2.7-2.840.29291680.23132568X-RAY DIFFRACTION99
2.84-3.020.28641460.24672568X-RAY DIFFRACTION100
3.02-3.250.31351400.23022596X-RAY DIFFRACTION100
3.25-3.580.27841240.21562582X-RAY DIFFRACTION100
3.58-4.10.18221320.18672567X-RAY DIFFRACTION99
4.1-5.160.20111190.15682578X-RAY DIFFRACTION100
5.16-44.650.22821410.18452571X-RAY DIFFRACTION99

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