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- PDB-8vig: EgtB-IV from Geminocystis sp. isolate SKYG4, an ergothioneine-bio... -

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Basic information

Entry
Database: PDB / ID: 8vig
TitleEgtB-IV from Geminocystis sp. isolate SKYG4, an ergothioneine-biosynthetic type IV sulfoxide synthase in complex with hercynine
ComponentsSulfoxide synthase EgtB-IV
KeywordsOXIDOREDUCTASE / ergothioneine / sulfoxide / sulfur / non-heme iron
Function / homology5-histidylcysteine sulfoxide synthase / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / N,N,N-trimethyl-histidine / : / 5-histidylcysteine sulfoxide synthase
Function and homology information
Biological speciesGeminocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsIreland, K.A. / Davis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1937971 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
CitationJournal: Structure / Year: 2024
Title: Structural insights into the convergent evolution of sulfoxide synthase EgtB-IV, an ergothioneine-biosynthetic homolog of ovothiol synthase OvoA.
Authors: Ireland, K.A. / Kayrouz, C.M. / Abbott, M.L. / Seyedsayamdost, M.R. / Davis, K.M.
History
DepositionJan 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 20, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sulfoxide synthase EgtB-IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7229
Polymers55,1341
Non-polymers5878
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-13 kcal/mol
Surface area16850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.177, 95.639, 101.392
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Sulfoxide synthase EgtB-IV


Mass: 55134.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geminocystis sp. (bacteria) / Strain: SKYG4 / Gene: ovoA, IGQ44_00985 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A978T1Y9

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Non-polymers , 5 types, 452 molecules

#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


Mass: 198.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H16N3O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.2 Å3/Da / Density % sol: 44 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.1 M Bis-Tris, pH 6.7, 23% PEG3350, 0.2 M magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.6→47.82 Å / Num. obs: 61246 / % possible obs: 99.81 % / Redundancy: 2 % / Biso Wilson estimate: 19.52 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.05404 / Rpim(I) all: 0.05404 / Rrim(I) all: 0.07642 / Net I/σ(I): 7.45
Reflection shellResolution: 1.6→1.657 Å / Redundancy: 2 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 5990 / CC1/2: 0.509 / CC star: 0.821 / Rpim(I) all: 0.677 / Rrim(I) all: 0.9574 / % possible all: 99.4

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Processing

Software
NameVersionClassification
XDSXDS-Apple_M1data reduction
XDSXDS-Apple_M1data scaling
PHASER1.20.1_4487phasing
Coot0.9.8.7model building
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→47.82 Å / SU ML: 0.2339 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2072 1997 3.26 %
Rwork0.186 59244 -
obs0.1867 61241 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→47.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3567 0 36 444 4047
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00693721
X-RAY DIFFRACTIONf_angle_d0.94355035
X-RAY DIFFRACTIONf_chiral_restr0.0607482
X-RAY DIFFRACTIONf_plane_restr0.0097647
X-RAY DIFFRACTIONf_dihedral_angle_d14.06741331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.45021420.43884159X-RAY DIFFRACTION99.49
1.64-1.680.35661380.34994144X-RAY DIFFRACTION99.37
1.68-1.730.33161420.27054166X-RAY DIFFRACTION99.68
1.73-1.790.23981400.22314193X-RAY DIFFRACTION99.61
1.79-1.850.2371340.21074160X-RAY DIFFRACTION99.74
1.85-1.930.25831400.22744207X-RAY DIFFRACTION99.84
1.93-2.020.23061480.20314182X-RAY DIFFRACTION99.91
2.02-2.120.20191440.16924208X-RAY DIFFRACTION99.98
2.12-2.260.20491360.16724240X-RAY DIFFRACTION100
2.26-2.430.21051390.17114233X-RAY DIFFRACTION100
2.43-2.670.19581540.17444269X-RAY DIFFRACTION99.98
2.67-3.060.21241370.17334263X-RAY DIFFRACTION100
3.06-3.860.16411500.15784318X-RAY DIFFRACTION99.91
3.86-47.820.17071530.16844502X-RAY DIFFRACTION99.91

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