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- PDB-5a6y: Structure of the LecB lectin from Pseudomonas aeruginosa strain P... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5a6y | |||||||||
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Title | Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with mannose-alpha1,3mannoside | |||||||||
![]() | FUCOSE-BINDING LECTIN PA-IIL | |||||||||
![]() | HYDROLASE / LECTIN / LECB | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Sommer, R. / Wagner, S. / Varrot, A. / Khaledi, A. / Haussler, S. / Imberty, A. / Titz, A. | |||||||||
![]() | ![]() Title: The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery. Authors: Sommer, R. / Wagner, S. / Varrot, A. / Nycholat, C.M. / Khaledi, A. / Haussler, S. / Paulson, J.C. / Imberty, A. / Titz, A. | |||||||||
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 | ![]() | 207.9 KB | Display | ![]() |
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PDB format | ![]() | 165.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.4 MB | Display | |
Data in XML | ![]() | 26.6 KB | Display | |
Data in CIF | ![]() | 40.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5a6qSC ![]() 5a6xC ![]() 5a6zC S: Starting model for refinement C: citing same article ( |
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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 domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 1 - 114 / Label seq-ID: 1 - 114
NCS ensembles :
NCS oper:
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 11676.710 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 2-115 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Sugars , 2 types, 4 molecules ![](data/chem/img/MAN.gif)
#2: Polysaccharide | #4: Sugar | ChemComp-MAN / | |
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-Non-polymers , 4 types, 691 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-CA / #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-SO4 / | #7: Water | ChemComp-HOH / | |
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-Details
Sequence details | NTERMINAL METHIONINE |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.38 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 24% PEG 8K 0.2M AMSO4 0.1M TRIS PH 8.5. 10% GLYCEROL WAS ADDED AS CRYOPROTECTANT |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 15, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8726 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→44.52 Å / Num. obs: 76843 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.4→1.42 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 5.4 / % possible all: 94.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 5A6Q Resolution: 1.4→44.52 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.747 / SU ML: 0.032 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.056 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 9.473 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→44.52 Å
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Refine LS restraints |
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