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- PDB-8qfq: Ergothioneine dioxygenase, variant H147A, from Thermocatellispora... -

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Basic information

Entry
Database: PDB / ID: 8qfq
TitleErgothioneine dioxygenase, variant H147A, 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 / : / TRIETHYLENE GLYCOL / Cysteine dioxygenase
Similarity search - Component
Biological speciesThermocatellispora tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 27, 2024Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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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)41,97813
Polymers41,2742
Non-polymers70411
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-16 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.419, 59.076, 134.629
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: 20636.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: H147A mutant
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 , 6 types, 154 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 143 / 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: Mar 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→44.4 Å / Num. obs: 42811 / % possible obs: 99.94 % / Redundancy: 2 % / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 17.95
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 4207 / CC1/2: 0.947

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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: 2.1→44.4 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1959 4.91 %
Rwork0.1801 --
obs0.1818 39907 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2366 0 41 143 2550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122442
X-RAY DIFFRACTIONf_angle_d1.4343310
X-RAY DIFFRACTIONf_dihedral_angle_d12.646336
X-RAY DIFFRACTIONf_chiral_restr0.092345
X-RAY DIFFRACTIONf_plane_restr0.01438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.32261550.23462656X-RAY DIFFRACTION100
2.15-2.210.22221640.20532692X-RAY DIFFRACTION100
2.21-2.280.24981180.19892752X-RAY DIFFRACTION100
2.28-2.350.23141350.18752706X-RAY DIFFRACTION100
2.35-2.430.20341400.17912706X-RAY DIFFRACTION100
2.43-2.530.24891410.17982720X-RAY DIFFRACTION100
2.53-2.650.24351550.17692711X-RAY DIFFRACTION100
2.65-2.790.22341420.17082707X-RAY DIFFRACTION100
2.79-2.960.23471250.18592760X-RAY DIFFRACTION100
2.96-3.190.23281180.18092697X-RAY DIFFRACTION100
3.19-3.510.21561420.17142707X-RAY DIFFRACTION100
3.51-4.020.21161290.17152717X-RAY DIFFRACTION100
4.02-5.060.15131440.16232714X-RAY DIFFRACTION100
5.06-44.40.21261510.19272703X-RAY DIFFRACTION100

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