[English] 日本語
Yorodumi- PDB-7blh: Structure of CBM BT3015C from Bacteroides thetaiotaomicron in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7blh | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with O-GalNAc core 1-Thr | ||||||
Components | family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron | ||||||
Keywords | SUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins / O-GalNAc core 1-Thr | ||||||
Function / homology | Function and homology information Viral BACON domain / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...Viral BACON domain / Bacteroidetes-Associated Carbohydrate-binding Often N-terminal / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold Similarity search - Domain/homology | ||||||
Biological species | Bacteroides thetaiotaomicron VPI-5482 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Costa, R.L. / Carvalho, A.L. | ||||||
Funding support | Portugal, 1items
| ||||||
Citation | Journal: To Be Published 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7blh.cif.gz | 59.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7blh.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7blh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7blh ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7blh | HTTPS FTP |
---|
-Related structure data
Related structure data | 7blgSC 7bljC 7blkC 7bllC S: Starting model for refinement C: citing same article (ref.) |
---|---|
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.) Bacteroides thetaiotaomicron VPI-5482 (bacteria) Gene: BT_3015 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A3D9 |
---|---|
#2: Polysaccharide | beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-THR / |
#4: Chemical | ChemComp-CA / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: Protein at 8mg/ml 0.2 M potassium formate and 20 % w/v PEG 6000 |
-Data collection
Diffraction | Mean temperature: 110 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5418 Å |
Detector | Type: BRUKER PHOTON 100 / Detector: CMOS / Date: Apr 17, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→23.65 Å / Num. obs: 15596 / % possible obs: 99.2 % / Redundancy: 5.82 % / Biso Wilson estimate: 13.5 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 19.09 |
Reflection shell | Resolution: 1.79→1.89 Å / Rmerge(I) obs: 0.256 / Num. unique obs: 2194 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BLG Resolution: 1.79→20.42 Å / SU ML: 0.1465 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 18.283 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: 9.92 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.79→20.42 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|