[English] 日本語
![](img/lk-miru.gif)
- PDB-7blg: Structure of CBM BT3015C from Bacteroides thetaiotaomicron in com... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 7blg | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with galactose | ||||||
![]() | family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron | ||||||
![]() | SUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins / galactose | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Costa, R.L. | ||||||
Funding support | ![]()
| ||||||
![]() | ![]() Title: Structural basis for mucin-type O-glycan recognition by proteins of a Bacteroides thetaiotaomicron polysaccharide utilization loci Authors: Costa, R.L. / Correia, V.G. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 56.9 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 31.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 816.4 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 816.4 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 13.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7blhC ![]() 7bljC ![]() 7blkC ![]() 7bllC ![]() 4a41S S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 17917.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3015 Production host: ![]() ![]() References: UniProt: Q8A3D9 |
---|---|
#2: Sugar | ChemComp-GAL / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 1.67 Å3/Da / Density % sol: 26.55 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein at 8mg/ml 0.12 M monosaccharides (0.2 M D Glucose; 0.2 M D Mannose; 0.2 M D Galactose; 0.2 M L Fucose; 0.2M D Xylose; 0.2 M N Acetyl D Glucosamine), 0.1 M buffer system (1.0 M pH 7.5 ...Details: Protein at 8mg/ml 0.12 M monosaccharides (0.2 M D Glucose; 0.2 M D Mannose; 0.2 M D Galactose; 0.2 M L Fucose; 0.2M D Xylose; 0.2 M N Acetyl D Glucosamine), 0.1 M buffer system (1.0 M pH 7.5 Sodium HEPES; MOPS) and 37.5% precipitant (25% v/v MPD; 25% w/v PEG 1000; 25% w/v PEG 3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 2, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→36.4 Å / Num. obs: 35097 / % possible obs: 88.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.92 Å2 / CC1/2: 0.99 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.17→1.19 Å / Num. unique obs: 1844 / CC1/2: 0.82 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 4a41 Resolution: 1.18→36.4 Å / SU ML: 0.0967 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.7806 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.18→36.4 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|