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Yorodumi- PDB-8vik: EgtB-IV from Crocosphaera subtropica, a type IV sulfoxide synthas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8vik | |||||||||
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Title | EgtB-IV from Crocosphaera subtropica, a type IV sulfoxide synthase involved in ergothioneine biosynthesis | |||||||||
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 / : / 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: 1.961 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 type IV sulfoxide synthase EgtB, 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 | 8vik.cif.gz | 212.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8vik.ent.gz | 151.1 KB | Display | PDB format |
PDBx/mmJSON format | 8vik.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8vik_validation.pdf.gz | 451 KB | Display | wwPDB validaton report |
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Full document | 8vik_full_validation.pdf.gz | 453.6 KB | Display | |
Data in XML | 8vik_validation.xml.gz | 34.9 KB | Display | |
Data in CIF | 8vik_validation.cif.gz | 51.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vi/8vik ftp://data.pdbj.org/pub/pdb/validation_reports/vi/8vik | HTTPS FTP |
-Related structure data
Related structure data | 8vigC 8vihC 8viiC 8vilC 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 , 5 types, 504 molecules
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 46.5 % / 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% PEG 3350 |
-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: 1.961→29.43 Å / Num. obs: 66735 / % possible obs: 97.37 % / Redundancy: 2 % / Biso Wilson estimate: 32.9 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.0487 / Rpim(I) all: 0.0487 / Rrim(I) all: 0.06888 / Net I/σ(I): 9.17 |
Reflection shell | Resolution: 1.961→2.031 Å / Redundancy: 2 % / Rmerge(I) obs: 0.5962 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5237 / CC1/2: 0.549 / CC star: 0.842 / Rpim(I) all: 0.5962 / Rrim(I) all: 0.8431 / % possible all: 76.57 |
-Processing
Software |
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Refinement | Method to determine structure: SIR / Resolution: 1.961→29.43 Å / SU ML: 0.2693 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.4199 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: 35.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.961→29.43 Å
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Refine LS restraints |
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LS refinement shell |
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