[English] 日本語
![](img/lk-miru.gif)
- PDB-6ve0: Crystal structure of reduced SfmD by soaking with sodium hydrosulfite -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 6ve0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of reduced SfmD by soaking with sodium hydrosulfite | ||||||
![]() | 3-methyl-L-tyrosine peroxygenase | ||||||
![]() | OXIDOREDUCTASE / Hydroxylase / Histidine-ligated heme | ||||||
Function / homology | 3-methyl-L-tyrosine peroxygenase / Tetracyclin repressor-like, C-terminal domain superfamily / antibiotic biosynthetic process / oxidoreductase activity / regulation of DNA-templated transcription / metal ion binding / HEME C / 3-methyl-L-tyrosine peroxygenase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shin, I. / Liu, A. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 73.4 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 50.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 351.7 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 351.8 KB | Display | |
Data in XML | ![]() | 1.4 KB | Display | |
Data in CIF | ![]() | 4.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vdpSC ![]() 6vdqC ![]() 6vdzC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 38232.902 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B0CN28, 3-methyl-L-tyrosine peroxygenase |
---|---|
#2: Chemical | ChemComp-HEC / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % |
---|---|
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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 3.15→50 Å / Num. obs: 6152 / % possible obs: 99.9 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.036 / Rrim(I) all: 0.109 / Χ2: 0.873 / Net I/σ(I): 6.2 / Num. measured all: 57538 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-
Processing
Software |
| ||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 6VDP Resolution: 3.15→49.01 Å / SU ML: 0.52 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 35.18
| ||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 166.05 Å2 / Biso mean: 110.441 Å2 / Biso min: 83.83 Å2 | ||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.15→49.01 Å
| ||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 4 / % reflection obs: 100 %
|