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Yorodumi- PDB-2boj: crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2boj | ||||||
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Title | crystal Structure of pseudomonas aeruginosa lectin (PA-IIL) complexed with methyl-B-D-Arabinopyranoside | ||||||
Components | PSEUDOMONAS AERUGINOSA LECTIN II | ||||||
Keywords | LECTIN / ARABINOSE / CALCIUM / LEWIS A / CYSTIC FIBROSIS | ||||||
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: 1.8 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. | ||||||
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 | 2boj.cif.gz | 114.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2boj.ent.gz | 87.8 KB | Display | PDB format |
PDBx/mmJSON format | 2boj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2boj_validation.pdf.gz | 467.8 KB | Display | wwPDB validaton report |
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Full document | 2boj_full_validation.pdf.gz | 469.5 KB | Display | |
Data in XML | 2boj_validation.xml.gz | 25.9 KB | Display | |
Data in CIF | 2boj_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2boj ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2boj | HTTPS FTP |
-Related structure data
Related structure data | 2bp6C 1uzvS 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-ARW / #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-SO4 / | #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: 1.74 Å3/Da / Density % sol: 29 % |
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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: ID14-2 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 10, 2002 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: SINGLE CRYSTAL DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→29.6 Å / Num. obs: 35769 / % possible obs: 97.9 % / Redundancy: 3.73 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.64 / % possible all: 89 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1UZV Resolution: 1.8→49.39 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.129 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED SIDE CHAINS ATOMS WERE MODELED WITH OCCUPANCIES LESS THAN 1.0
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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: 11.43 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→49.39 Å
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Refine LS restraints |
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