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Yorodumi- PDB-6q87: Structure of Fucosylated D-antimicrobial peptide SB10 in complex ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q87 | ||||||
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Title | Structure of Fucosylated D-antimicrobial peptide SB10 in complex with the Fucose-binding lectin PA-IIL at 2.541 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: 2.541 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 | 6q87.cif.gz | 62.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q87.ent.gz | 45.2 KB | Display | PDB format |
PDBx/mmJSON format | 6q87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q87_validation.pdf.gz | 453.8 KB | Display | wwPDB validaton report |
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Full document | 6q87_full_validation.pdf.gz | 454.4 KB | Display | |
Data in XML | 6q87_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | 6q87_validation.cif.gz | 8.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q8/6q87 ftp://data.pdbj.org/pub/pdb/validation_reports/q8/6q87 | HTTPS FTP |
-Related structure data
Related structure data | 6q6wC 6q6xC 6q77C 6q79C 6q85C 6q86C 6q8dC 6q8gC 6q8hC 6s5pC 1oxcS C: citing same article (ref.) S: Starting model for refinement |
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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
-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(DE3) (bacteria) / Variant (production host): Gold pLysS AG / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS |
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#2: Polypeptide(D) | Mass: 1545.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Sugar | ChemComp-ZDC / |
-Non-polymers , 3 types, 15 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: 4.57 Å3/Da / Density % sol: 73.09 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 5% v/v Tacsimate pH 7.0, 0.1 M HEPES pH 7.0 ,10% w/v Polyethylene glycol monomethyl ether 5,000 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000031 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jul 6, 2018 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000031 Å / Relative weight: 1 |
Reflection | Resolution: 2.54→45.419 Å / Num. obs: 15464 / % possible obs: 99.37 % / Redundancy: 6.99 % / Rrim(I) all: 0.076 / Net I/σ(I): 12.74 |
Reflection shell | Resolution: 2.5414→2.7006 Å / % possible all: 98 |
-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OXC Resolution: 2.541→45.419 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.66 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 118.69 Å2 / Biso mean: 69.0029 Å2 / Biso min: 42.22 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.541→45.419 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: 6
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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