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Yorodumi- PDB-7oln: Structure of the N-terminal domain of BC2L-C lectin (1-131) in co... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7oln | ||||||
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Title | Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with Lewis y antigen | ||||||
Components | Lectin | ||||||
Keywords | SUGAR BINDING PROTEIN / Bacterial lectin / Fucosides / Blood group antigen / Human oligosaccharide | ||||||
Function / homology | Lectin Bc2l-C, N-terminal / : / Bc2l-C, N-terminal domain / Calcium-mediated lectin / Calcium-mediated lectin superfamily / Fucose-binding lectin II (PA-IIL) / identical protein binding / Lectin Function and homology information | ||||||
Biological species | Burkholderia cenocepacia (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Bermeo, R. / Varrot, A. | ||||||
Funding support | France, 1items
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Citation | Journal: To Be Published Title: Structure of the N-terminal domain of BC2L-C lectin (1-131) in complex with Lewis y antigen Authors: Bermeo, R. / Varrot, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7oln.cif.gz | 46.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7oln.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7oln.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ol/7oln ftp://data.pdbj.org/pub/pdb/validation_reports/ol/7oln | HTTPS FTP |
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-Related structure data
Related structure data | 2wq4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 14010.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610) (bacteria) Strain: ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610 Gene: BCAM0185 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B4EH86 |
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#2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose Type: oligosaccharide / Mass: 837.771 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
#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: 1.96 Å3/Da / Density % sol: 37.18 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: sodium citrate 1.2M |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→36.88 Å / Num. obs: 8958 / % possible obs: 100 % / Redundancy: 15.6 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.026 / Rrim(I) all: 0.077 / Net I/σ(I): 23.8 |
Reflection shell | Resolution: 1.92→1.97 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 601 / CC1/2: 0.982 / Rpim(I) all: 0.143 / Rrim(I) all: 0.424 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2wq4 Resolution: 1.92→36.88 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.876 / SU ML: 0.085 / Cross valid method: FREE R-VALUE / ESU R: 0.159 / ESU R Free: 0.138 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.301 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→36.88 Å
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Refine LS restraints |
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LS refinement shell |
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