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Yorodumi- PDB-6vdz: Crystal structure of reduced SfmD by soaking with sodium hydrosulfite -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vdz | ||||||
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Title | Crystal structure of reduced SfmD by soaking with sodium hydrosulfite | ||||||
Components | 3-methyl-L-tyrosine peroxygenase | ||||||
Keywords | OXIDOREDUCTASE / Hydroxylase / Histidine-ligated heme | ||||||
Function / homology | 3-methyl-L-tyrosine peroxygenase / Tetracyclin repressor-like, C-terminal domain superfamily / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding / HEME C / 3-methyl-L-tyrosine peroxygenase Function and homology information | ||||||
Biological species | Streptomyces lavendulae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | ||||||
Authors | Shin, I. / Liu, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Chem Sci / Year: 2021 Title: A novel catalytic heme cofactor in SfmD with a single thioether bond and a bis -His ligand set revealed by a de novo crystal structural and spectroscopic study. Authors: Shin, I. / Davis, I. / Nieves-Merced, K. / Wang, Y. / McHardy, S. / Liu, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vdz.cif.gz | 72.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vdz.ent.gz | 50.1 KB | Display | PDB format |
PDBx/mmJSON format | 6vdz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vd/6vdz ftp://data.pdbj.org/pub/pdb/validation_reports/vd/6vdz | HTTPS FTP |
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-Related structure data
Related structure data | 6vdpSC 6vdqC 6ve0C S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38232.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces lavendulae (bacteria) / Gene: sfmD / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: B0CN28, 3-methyl-L-tyrosine peroxygenase |
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#2: Chemical | ChemComp-HEC / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.48 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 0.1 M Tris pH 8.5, 0.2 M magnesium chloride, 30% PEG 4000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.95→50 Å / Num. obs: 7467 / % possible obs: 99 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.03 / Rrim(I) all: 0.088 / Χ2: 1.028 / Net I/σ(I): 8.1 / Num. measured all: 58396 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6VDP Resolution: 2.95→49.36 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 39.03
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 138.13 Å2 / Biso mean: 106.9007 Å2 / Biso min: 96.71 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.95→49.36 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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