[English] 日本語

- PDB-8qrz: Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 8qrz | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type | ||||||||||||
![]() | Sugar phosphate isomerase | ||||||||||||
![]() | LYASE / bacterial C-glucosyl deglycosidase / C-C bond cleavage / C-glucosyl flavonoids / Microbacterium testaceum NS220 / plant endosymbiont / N-terminal DUF6379 beta-sandwich domain / C-terminal TIM barrel domain / homodimer | ||||||||||||
Function / homology | ![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Furlanetto, V. / Kalyani, D.C. / Divne, C. | ||||||||||||
Funding support | ![]()
| ||||||||||||
![]() | ![]() Title: Microbacterium testaceum C-glucosyl deglycosidase (CGD), wild type Authors: Furlanetto, V. / Kalyani, D.C. / Srivastava, V. / Hallberg, B.M. / Ezcurra, I. / Divne, C. | ||||||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 347.5 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 282.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 2.9 MB | Display | |
Data in XML | ![]() | 73.2 KB | Display | |
Data in CIF | ![]() | 94.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homology ![]() |
---|
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 48768.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-RB / #3: Water | ChemComp-HOH / | Has ligand of interest | Y | Has protein modification | N | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.59 Å3/Da / Density % sol: 52.5 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1 M PIPES pH 7.0, 25% (w/v) PEGSH (PEG SMEAR HIGH), 0.1 M rubidium(I) chloride, 0.1 M magnesium(II) formate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS EIGER2 XE CdTe 9M / Detector: PIXEL / Date: Aug 16, 2023 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.61992 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.29 Å / Num. obs: 128896 / % possible obs: 98.8 % / Redundancy: 4.1 % / Biso Wilson estimate: 31.55 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.111 / Net I/σ(I): 8.4 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.034 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 17550 / CC1/2: 0.458 / % possible all: 98.7 |
-
Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]()
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→39.91 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|