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Yorodumi- PDB-6q6w: Structure of Fucosylated D-antimicrobial peptide SB5 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q6w | ||||||
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Title | Structure of Fucosylated D-antimicrobial peptide SB5 in complex with the Fucose-binding lectin PA-IIL at 1.438 Angstrom resolution | ||||||
Components |
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Keywords | ANTIBIOTIC / Antimicrobial / Lectin / Complex | ||||||
Function / homology | Function and homology information single-species biofilm formation / carbohydrate binding / metal ion binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.438 Å | ||||||
Authors | Baeriswyl, S. / Stocker, A. / Reymond, J.L. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Acs Chem.Biol. / Year: 2019 Title: X-ray Crystal Structures of Short Antimicrobial Peptides as Pseudomonas aeruginosa Lectin B Complexes. Authors: Baeriswyl, S. / Gan, B.H. / Siriwardena, T.N. / Visini, R. / Robadey, M. / Javor, S. / Stocker, A. / Darbre, T. / Reymond, J.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6q6w.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q6w.ent.gz | 48 KB | Display | PDB format |
PDBx/mmJSON format | 6q6w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q6w_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 6q6w_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 6q6w_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | 6q6w_validation.cif.gz | 11.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q6/6q6w ftp://data.pdbj.org/pub/pdb/validation_reports/q6/6q6w | HTTPS FTP |
-Related structure data
Related structure data | 6q6xC 6q77C 6q79C 6q85C 6q86C 6q87C 6q8dC 6q8gC 6q8hC 6s5pC 1oxcS 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 on special symmetry positions |
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-Components
-Protein / Polypeptide(D) / Sugars , 3 types, 3 molecules AB
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Fucose-binding lectin PA-IIL Lectin B from Pseudomonas aeruginosa Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: lecB, C0043_24310, C0044_25260, C0046_23510, CAZ10_21840, CW299_25270, DI492_13230, DT376_00595, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453 Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS |
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#2: Polypeptide(D) | Mass: 1416.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Fucosylated D-antimicrobial peptide SB5 / Source: (synth.) synthetic construct (others) |
#4: Sugar | ChemComp-ZDC / |
-Non-polymers , 3 types, 132 molecules
#3: Chemical | #5: Chemical | ChemComp-NH2 / | #6: 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: 3.12 Å3/Da / Density % sol: 60.61 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 1.5 M Ammonium sulfate, 0.1 M Tris pH 8.5, 12% v/v Glycerol |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.03679 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 18, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.03679 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.438→47.462 Å / Num. all: 31196 / Num. obs: 31196 / % possible obs: 99.2 % / Redundancy: 9.2 % / Rpim(I) all: 0.02 / Rrim(I) all: 0.062 / Rsym value: 0.058 / Net I/av σ(I): 8.5 / Net I/σ(I): 17.4 / Num. measured all: 286261 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OXC Resolution: 1.438→47.462 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.27 / Phase error: 20.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 67.44 Å2 / Biso mean: 28.706 Å2 / Biso min: 16.47 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.438→47.462 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20
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