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- PDB-7blh: Structure of CBM BT3015C from Bacteroides thetaiotaomicron in com... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7blh | ||||||
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Title | Structure of CBM BT3015C from Bacteroides thetaiotaomicron in complex with O-GalNAc core 1-Thr | ||||||
![]() | family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron | ||||||
![]() | SUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins / O-GalNAc core 1-Thr | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Costa, R.L. / Carvalho, A.L. | ||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 59.7 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 9.8 KB | Display | |
Data in CIF | ![]() | 14.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7blgSC ![]() 7bljC ![]() 7blkC ![]() 7bllC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components
#1: Protein | Mass: 17917.562 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: BT_3015 Production host: ![]() ![]() References: UniProt: Q8A3D9 |
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#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: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.79 % |
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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 |
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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 |
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Processing
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Refinement | Method to determine structure: ![]() 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
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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
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Refine LS restraints |
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LS refinement shell |
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