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- PDB-5mih: Crystal structure of the lectin LecA from Pseudomonas aeruginosa ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5mih | ||||||
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Title | Crystal structure of the lectin LecA from Pseudomonas aeruginosa in complex with a phenyl-epoxy-galactopyranoside | ||||||
![]() | PA-I galactophilic lectin | ||||||
![]() | SUGAR BINDING PROTEIN / LECTIN / GALACTOSE BINDING PROTEIN / covalent lectin inhibition | ||||||
Function / homology | ![]() heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / carbohydrate binding / periplasmic space / cell surface / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wagner, S. / Hauk, D. / Hofmann, M. / Joachim, I. / Sommer, R. / Muller, R. / Imberty, A. / Varrot, A. / Titz, A. | ||||||
![]() | ![]() Title: Covalent Lectin Inhibition and Application in Bacterial Biofilm Imaging. Authors: Wagner, S. / Hauck, D. / Hoffmann, M. / Sommer, R. / Joachim, I. / Muller, R. / Imberty, A. / Varrot, A. / Titz, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 122.2 KB | Display | ![]() |
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PDB format | ![]() | 93.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 28.6 KB | Display | |
Data in CIF | ![]() | 41.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1okoS 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 domain:
NCS domain segments: Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 1 - 121 / Label seq-ID: 1 - 121
NCS ensembles :
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Components
#1: Protein | Mass: 12770.137 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: N TERMINAL METHIONINE PROCESSED Source: (gene. exp.) ![]() Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: lecA, pa1L, PA2570 / Production host: ![]() ![]() #2: Chemical | ChemComp-CA / #3: Sugar | ChemComp-7NU / #4: Chemical | ChemComp-ETE / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.74 % / Description: parallelepipoid |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 25% peg 2KMME 100mM sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→27.3 Å / Num. obs: 36960 / % possible obs: 98.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/av σ(I): 14.4 / Net I/σ(I): 19.8 |
Reflection shell | Resolution: 1.8→1.84 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.2 / CC1/2: 0.954 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1OKO Resolution: 1.8→27.3 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.853 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.127 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.187 Å2
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Refinement step | Cycle: 1 / Resolution: 1.8→27.3 Å
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Refine LS restraints |
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