+Open data
-Basic information
Entry | Database: PDB / ID: 3zw1 | |||||||||
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Title | Structure of Bambl lectine in complex with lewix x antigen | |||||||||
Components | (BAMBL LECTIN) x 2 | |||||||||
Keywords | SUGAR BINDING PROTEIN / FUCOSE BINDING LECTIN | |||||||||
Function / homology | Lipocalin - #190 / Fucose-specific lectin / Fungal fucose-specific lectin / Lipocalin / Beta Barrel / Mainly Beta / alpha-D-galactopyranose / Uncharacterized protein / Fucose-binding lectin protein Function and homology information | |||||||||
Biological species | BURKHOLDERIA AMBIFARIA (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: Plos One / Year: 2013 Title: Deciphering the Glycan Preference of Bacterial Lectins by Glycan Array and Molecular Docking with Validation by Microcalorimetry and Crystallography. Authors: Topin, J. / Arnaud, J. / Sarkar, A. / Audfray, A. / Gillon, E. / Perez, S. / Jamet, H. / Varrot, A. / Imberty, A. / Thomas, A. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zw1.cif.gz | 59.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zw1.ent.gz | 41.6 KB | Display | PDB format |
PDBx/mmJSON format | 3zw1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zw/3zw1 ftp://data.pdbj.org/pub/pdb/validation_reports/zw/3zw1 | HTTPS FTP |
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-Related structure data
Related structure data | 3zw0S 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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2 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.94918, 0.24442, -0.19829), Vector: |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 9403.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: B1Z019, UniProt: Q0B4G1*PLUS |
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#2: Protein | Mass: 9387.166 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BURKHOLDERIA AMBIFARIA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYS / References: UniProt: B1Z019, UniProt: Q0B4G1*PLUS |
-Sugars , 3 types, 5 molecules
#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-GLA / | |
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-Non-polymers , 1 types, 237 molecules
#6: 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: 2.3 Å3/Da / Density % sol: 46.54 % / Description: NONE |
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Crystal grow | pH: 5 Details: 28 % PEG 6000, 100MM SODIUM ACETATE PH 5.0, 200MM TRISODIUM CITRATE. 10% ETHYLENE GLYCOL WAD ADDED AS CRYOPROTECTANT PRIOR TO FREEZING |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.1399 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 7, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1399 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→40.72 Å / Num. obs: 23162 / % possible obs: 96.2 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.6 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 7.9 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZW0 Resolution: 1.6→40.72 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.263 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. DISORDERED SIDE CHAINS WERE MODELED STEREOCHEMICALLY
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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: 12.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→40.72 Å
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Refine LS restraints |
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