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Yorodumi- PDB-8vil: EgtB-IV from Crocosphaera subtropica, an ergothioneine-biosynthet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vil | |||||||||
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Title | EgtB-IV from Crocosphaera subtropica, an ergothioneine-biosynthetic type IV sulfoxide synthase in complex with N,N-dimethyl-histidine | |||||||||
Components | Sulfoxide synthase EgtB-IV | |||||||||
Keywords | OXIDOREDUCTASE / ergothioneine / sulfoxide / sulfur / non-heme iron | |||||||||
Function / homology | 5-histidylcysteine sulfoxide synthase / : / Sulfatase-modifying factor enzyme / Sulfatase-modifying factor enzyme 1 / Sulfatase-modifying factor enzyme superfamily / C-type lectin fold / N,N-dimethyl-L-histidine / : / Sulfatase-modifying factor enzyme domain-containing protein Function and homology information | |||||||||
Biological species | Crocosphaera subtropica ATCC 51142 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 1.95 Å | |||||||||
Authors | Ireland, K.A. / Davis, K.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8vil.cif.gz | 216 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vil.ent.gz | 152.5 KB | Display | PDB format |
PDBx/mmJSON format | 8vil.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vil_validation.pdf.gz | 803.7 KB | Display | wwPDB validaton report |
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Full document | 8vil_full_validation.pdf.gz | 806 KB | Display | |
Data in XML | 8vil_validation.xml.gz | 35.8 KB | Display | |
Data in CIF | 8vil_validation.cif.gz | 52.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/8vil ftp://data.pdbj.org/pub/pdb/validation_reports/vi/8vil | HTTPS FTP |
-Related structure data
Related structure data | 8vigC 8vihC 8viiC 8vikC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | 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, 527 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-EDO / #6: Chemical | ChemComp-AVI / | #7: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.6 % / Description: Thin plates |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.1 Details: 0.1 M Bis-Tris, pH 6.1, 0.18 M ammonium acetate, 25% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å |
Detector | Type: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Oct 19, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9686 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→29.43 Å / Num. obs: 68198 / % possible obs: 97.86 % / Redundancy: 1.9 % / Biso Wilson estimate: 28.99 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05831 / Rpim(I) all: 0.05831 / Rrim(I) all: 0.08246 / Net I/σ(I): 10.1 |
Reflection shell | Resolution: 1.95→2.02 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.646 / Mean I/σ(I) obs: 1.25 / Num. unique obs: 6103 / CC1/2: 0.569 / CC star: 0.852 / Rpim(I) all: 0.646 / Rrim(I) all: 0.9136 / % possible all: 86.03 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 1.95→29.43 Å / SU ML: 0.2391 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.2847 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→29.43 Å
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Refine LS restraints |
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LS refinement shell |
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