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- PDB-8vih: EgtB-IV from Crocosphaera subtropica, an ergothioneine-biosynthet... -

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Basic information

Entry
Database: PDB / ID: 8vih
TitleEgtB-IV from Crocosphaera subtropica, an ergothioneine-biosynthetic type IV sulfoxide synthase in complex with hercynine
ComponentsSulfoxide synthase EgtB-IV
KeywordsOXIDOREDUCTASE / ergothioneine / sulfoxide / sulfur / non-heme iron
Function / homology
Function and homology information


formylglycine-generating oxidase activity / metal ion binding
Similarity search - Function
5-histidylcysteine sulfoxide synthase / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1-like domain / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold
Similarity search - Domain/homology
N,N,N-trimethyl-histidine / : / Sulfatase-modifying factor enzyme-like domain-containing protein
Similarity search - Component
Biological speciesCrocosphaera subtropica ATCC 51142 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsIreland, K.A. / Davis, K.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM147557 United States
National Science Foundation (NSF, United States)1937971 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

Downloads & links

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Assembly

Deposited unit
A: Sulfoxide synthase EgtB-IV
B: Sulfoxide synthase EgtB-IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,66215
Polymers109,7272
Non-polymers93513
Water15,385854
1
A: Sulfoxide synthase EgtB-IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3628
Polymers54,8631
Non-polymers4997
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sulfoxide synthase EgtB-IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3007
Polymers54,8631
Non-polymers4376
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.197, 94.511, 83.747
Angle α, β, γ (deg.)90.000, 100.160, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Sulfoxide synthase EgtB-IV


Mass: 54863.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Crocosphaera subtropica ATCC 51142 (bacteria)
Gene: cce_1041 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B1WTS6

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Non-polymers , 6 types, 867 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-AVJ / N,N,N-trimethyl-histidine / Hercynine


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


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 854 / 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: 2.3 Å3/Da / Density % sol: 46.6 % / Description: Thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.1 M Bis-Tris, pH 5.9, 23% PEG3350, 0.2 M ammonium acetate

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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: 1.55→47.26 Å / Num. obs: 136888 / % possible obs: 99.12 % / Redundancy: 1.9 % / Biso Wilson estimate: 18.99 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.0513 / Rpim(I) all: 0.0513 / Rrim(I) all: 0.07255 / Net I/σ(I): 7.38
Reflection shellResolution: 1.55→1.605 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.5944 / Mean I/σ(I) obs: 1.13 / Num. unique obs: 13254 / CC1/2: 0.506 / CC star: 0.82 / Rpim(I) all: 0.5944 / Rrim(I) all: 0.8406 / % possible all: 96.69

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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: 1.55→47.26 Å / SU ML: 0.2469 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.2149
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1983 1999 1.46 %
Rwork0.1796 135076 -
obs0.1799 136711 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.37 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7069 0 54 854 7977
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01637382
X-RAY DIFFRACTIONf_angle_d1.324810056
X-RAY DIFFRACTIONf_chiral_restr0.0881019
X-RAY DIFFRACTIONf_plane_restr0.0111295
X-RAY DIFFRACTIONf_dihedral_angle_d14.00512570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.46751300.46518834X-RAY DIFFRACTION90.98
1.59-1.630.40011440.3749684X-RAY DIFFRACTION99.44
1.63-1.680.30751440.29149727X-RAY DIFFRACTION99.68
1.68-1.730.28941440.23399710X-RAY DIFFRACTION99.77
1.73-1.790.22951430.20589712X-RAY DIFFRACTION99.78
1.79-1.860.24731440.19789693X-RAY DIFFRACTION99.73
1.86-1.950.23321440.20439745X-RAY DIFFRACTION99.74
1.95-2.050.22791440.19259704X-RAY DIFFRACTION99.7
2.05-2.180.17581430.16289692X-RAY DIFFRACTION99.3
2.18-2.350.20761440.16579678X-RAY DIFFRACTION99.15
2.35-2.580.20351430.16739682X-RAY DIFFRACTION98.96
2.59-2.960.16981430.1679702X-RAY DIFFRACTION99.13
2.96-3.730.16261430.15559698X-RAY DIFFRACTION98.96
3.73-47.260.1511460.14569815X-RAY DIFFRACTION98.75

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