[English] 日本語
![](img/lk-miru.gif)
- PDB-5xto: Crystal structure of baculoviral sulfhydryl oxidase P33 (H114A mutant) -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5xto | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of baculoviral sulfhydryl oxidase P33 (H114A mutant) | ||||||
![]() | FAD-linked sulfhydryl oxidase | ||||||
![]() | OXIDOREDUCTASE / sulfhydryl oxidase | ||||||
Function / homology | FAD-linked sulfhydryl oxidase / Baculovirus P33 / thiol oxidase / thiol oxidase activity / host cell cytoplasm / host cell nucleus / FLAVIN-ADENINE DINUCLEOTIDE / FAD-linked sulfhydryl oxidase![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kuang, W. / Hu, Z. / Gong, P. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Three Conserved Regions in Baculovirus Sulfhydryl Oxidase P33 Are Critical for Enzymatic Activity and Function Authors: Kuang, W. / Zhang, H. / Wang, M. / Zhou, N.Y. / Deng, F. / Wang, H. / Gong, P. / Hu, Z. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 214.8 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 170.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
---|
-Related structure data
Related structure data | ![]() 5xkiC ![]() 5xtnC ![]() 5xtpC ![]() 5xtqC ![]() 5xtrC ![]() 3qzyS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 34459.871 Da / Num. of mol.: 4 / Mutation: H114A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: P33, ORF92 / Plasmid: pET28 / Production host: ![]() ![]() #2: Chemical | ChemComp-FAD / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 47 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2 / Details: PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.555→60 Å / Num. obs: 37851 / % possible obs: 93.2 % / Redundancy: 3.8 % / Biso Wilson estimate: 41.16 Å2 / Rmerge(I) obs: 0.079 / Χ2: 0.98 / Net I/σ(I): 6.4 / Num. measured all: 142090 |
Reflection shell | Resolution: 2.56→2.65 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.484 / Num. unique all: 4044 / CC1/2: 0.999 / Χ2: 0.992 / % possible all: 91.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 3QZY Resolution: 2.56→37.55 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 33.4
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 82.91 Å2 / Biso mean: 39.56 Å2 / Biso min: 17.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.56→37.55 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
|