+Open data
-Basic information
Entry | Database: PDB / ID: 7blk | ||||||
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Title | Structure of CBM BT3015C from Bacteroides thetaiotaomicron | ||||||
Components | family 32 carbohydrate-binding module from Bacteroides thetaiotaomicron | ||||||
Keywords | SUGAR BINDING PROTEIN / Bacteroides thetaiotaomicron / carbohydrate-binding module / gut microbiome / mucins | ||||||
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 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å | ||||||
Authors | Costa, R.L. | ||||||
Funding support | Portugal, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7blk.cif.gz | 49.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7blk.ent.gz | 32.1 KB | Display | PDB format |
PDBx/mmJSON format | 7blk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bl/7blk ftp://data.pdbj.org/pub/pdb/validation_reports/bl/7blk | HTTPS FTP |
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-Related structure data
Related structure data | 7blgSC 7blhC 7bljC 7bllC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-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.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria) Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_3015 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: Q8A3D9 |
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#2: Chemical | ChemComp-CA / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.65 Å3/Da / Density % sol: 25.46 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 8 mg/ml 30% w/v PEG 2000 monomethyl ether and 0.1 M potassium thiocyanate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å |
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: 1.06→36.24 Å / Num. obs: 84450 / % possible obs: 98.6 % / Redundancy: 3 % / Biso Wilson estimate: 12.64 Å2 / CC1/2: 0.99 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 1.06→1.08 Å / Num. unique obs: 2611 / CC1/2: 0.92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7BLG Resolution: 1.06→36.24 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.94 / Phase error: 19.78 / Stereochemistry target values: ML
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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 max: 58.23 Å2 / Biso mean: 16.6276 Å2 / Biso min: 8.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.06→36.24 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 29
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