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Yorodumi- PDB-2bp6: crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bp6 | ||||||
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Title | crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with a-L-Galactopyranoside | ||||||
Components | PSEUDOMONAS AERUGINOSA LECTIN II | ||||||
Keywords | LECTIN / GALACTOSE / CALCIUM / PSEUDOMONAS AERUGINOSA | ||||||
Function / homology | Function and homology information single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | PSEUDOMONAS AERUGINOSA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Sabin, C.D. / Mitchell, E.P. / Wimmerova, M. / Imberty, A. | ||||||
Citation | Journal: FEBS Lett. / Year: 2006 Title: Binding of Different Monosaccharides by Lectin Pa-Iil from Pseudoman Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures. Authors: Sabin, C.D. / Mitchell, E.P. / Pokarna, M. / Gautier, C. / Utille, J.-P. / Wimmerova, M. / Imberty, A. #1: Journal: Proteins: Struct.,Funct., Genet. / Year: 2005 Title: High Affinity Fucose Binding of Pseudomonas Aeruginosa Lectin Pa-Iil: 1.0 A Resolution Crystal Structure of the Complex Combined with Thermodynamics and Computational Chemistry Approaches Authors: Mitchell, E. / Sabin, C.D. / Snajdrova, L. / Pokorna, M. / Perret, S. / Gautier, C. / Hofr, C. / Gilboa-Garber, N. / Koca, J. / Wimmerova, M. / Imberty, A. #2: Journal: Nat.Struct.Biol. / Year: 2002 Title: Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients Authors: Mitchell, E. / Houles, C. / Sudakevitz, D. / Wimmerova, M. / Gautier, C. / Perez, S. / Wu, A.M. / Gilboa-Garber, N. / Imberty, A. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bp6.cif.gz | 109.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bp6.ent.gz | 83.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bp6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bp/2bp6 ftp://data.pdbj.org/pub/pdb/validation_reports/bp/2bp6 | HTTPS FTP |
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-Related structure data
Related structure data | 2bojC 1uzvS 1w38 1w43 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: 11734.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PET25PAIIL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HYN5 #2: Sugar | ChemComp-GXL / #3: Chemical | ChemComp-CA / #4: Chemical | #5: 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: 1.9 Å3/Da / Density % sol: 34.72 % |
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Crystal grow | pH: 8.5 Details: TRIS HCL 0.1M, PH8.5, 1.75 M AMMONIUM SULFATE, pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Mar 17, 2003 / Details: MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→19.43 Å / Num. obs: 63528 / % possible obs: 97 % / Redundancy: 3.82 % / Biso Wilson estimate: 10.28 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.35 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3.08 / % possible all: 95.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UZV Resolution: 1.5→19.43 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.992 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.22 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19.43 Å
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Refine LS restraints |
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