+Open data
-Basic information
Entry | Database: PDB / ID: 3zzv | |||||||||
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Title | BambL complexed with Htype2 tetrasaccharide | |||||||||
Components | BAMBL LECTIN | |||||||||
Keywords | SUGAR BINDING PROTEIN / CYSTIC FIBROSIS / BETA-PROPELLER / HUMAN HISTO-BLOOD GROUP | |||||||||
Function / homology | Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / H type 2 antigen, beta anomer / alpha-L-fucopyranose / Fucose-binding lectin protein Function and homology information | |||||||||
Biological species | BURKHOLDERIA AMBIFARIA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å | |||||||||
Authors | Audfray, A. / Claudinon, J. / Abounit, S. / Ruvoen-Clouet, N. / Larson, G. / Wimmerova, M. / LePendu, J. / Romer, W. / Varrot, A. / Imberty, A. | |||||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Fucose-Binding Lectin from Opportunistic Pathogen Burkholderia Ambifaria Binds to Both Plant and Human Oligosaccharidic Epitopes. Authors: Audfray, A. / Claudinon, J. / Abounit, S. / Ruvoen-Clouet, N. / Larson, G. / Smith, D.F. / Wimmerova, M. / Le Pendu, J. / Romer, W. / Varrot, A. / Imberty, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zzv.cif.gz | 73 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zzv.ent.gz | 54.4 KB | Display | PDB format |
PDBx/mmJSON format | 3zzv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzv ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzv | HTTPS FTP |
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-Related structure data
Related structure data | 3zw0C 3zw2C 3zweC 3wz0S C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 9387.166 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Strain: AMMD / Plasmid: PET25 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0B4G1 #2: Polysaccharide | alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / H type 2 antigen / beta anomer #3: Sugar | ChemComp-FUC / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.29 Å3/Da / Density % sol: 46.28 % / Description: NONE |
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Crystal grow | pH: 7.5 / Details: pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 22, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.68→73.28 Å / Num. obs: 26045 / % possible obs: 96.9 % / Observed criterion σ(I): 3 / Redundancy: 3.5 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.68→1.77 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 1.9 / % possible all: 81.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3WZ0 Resolution: 1.68→73.28 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.751 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.817 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→73.28 Å
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Refine LS restraints |
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