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- PDB-4ut5: Crystal structure of the LecB lectin from Pseudomonas aeruginosa ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ut5 | |||||||||
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Title | Crystal structure of the LecB lectin from Pseudomonas aeruginosa strain PA7 in complex with lewis a tetrasaccharide | |||||||||
![]() | LECB LECTIN | |||||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / TETRAMERIC / LEWIS A / LECB VARIANT | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Boukerb, A.M. / Decor, A. / Tabaroni, R. / Varrot, A. / Debentzmann, S. / Vidal, S. / Imberty, A. / Cournoyer, B. | |||||||||
![]() | ![]() Title: Genomic Rearrangements and Functional Diversification of Leca and Lecb Lectin-Coding Regions Impacting the Efficacy of Glycomimetics Directed Against Pseudomonas Aeruginosa. Authors: Boukerb, A.M. / Decor, A. / Ribun, S. / Tabaroni, R. / Rousset, A. / Commin, L. / Buff, S. / Doleans-Jordheim, A. / Vidal, S. / Varrot, A. / Imberty, A. / Cournoyer, B. | |||||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 117.4 KB | Display | ![]() |
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PDB format | ![]() | 90.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1gztS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 11659.705 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 4 types, 5 molecules ![](data/chem/img/GAL.gif)
#2: Polysaccharide | beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose- ...beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-GAL / | |
-Non-polymers , 2 types, 652 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-CA / #7: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.08 % / Description: NONE |
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Crystal grow | pH: 4.6 Details: 14% PEG6K, 0.2M LITHIUM CHLORIDE AND 0.1M SODIUM ACETATE PH 4.6. CRYO WITH 26% PEG 6K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 7, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9205 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→42.23 Å / Num. obs: 40169 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1GZT Resolution: 1.75→42.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.178 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY THE NUMBERING IS SHEFTED BY ONE COMPARE TO THE UNIPROT ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY DISORDERED REGIONS WERE MODELED STEREOCHEMICALLY THE NUMBERING IS SHEFTED BY ONE COMPARE TO THE UNIPROT SEQUENCE SINCE THE NTERMINAL METHIONINE IS NOT PRESENT IN THE MATURE PROTEIN
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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: 12.49 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→42.23 Å
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Refine LS restraints |
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