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Yorodumi- PDB-6q79: Structure of Fucosylated D-antimicrobial peptide SB4 in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6q79 | ||||||
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Title | Structure of Fucosylated D-antimicrobial peptide SB4 in complex with the Fucose-binding lectin PA-IIL at 2.009 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: 2.009 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 | 6q79.cif.gz | 203.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6q79.ent.gz | 166.3 KB | Display | PDB format |
PDBx/mmJSON format | 6q79.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6q79_validation.pdf.gz | 490.7 KB | Display | wwPDB validaton report |
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Full document | 6q79_full_validation.pdf.gz | 493.8 KB | Display | |
Data in XML | 6q79_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 6q79_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q7/6q79 ftp://data.pdbj.org/pub/pdb/validation_reports/q7/6q79 | HTTPS FTP |
-Related structure data
Related structure data | 6q6wC 6q6xC 6q77C 6q85C 6q86C 6q87C 6q8dC 6q8gC 6q8hC 6s5pC 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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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Polypeptide(D) , 2 types, 4 molecules EHFG
#2: Polypeptide(D) | Mass: 1545.013 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Fucosylated D-antimicrobial peptide SB4, complete alpha helical sequence Source: (synth.) synthetic construct (others) #3: Polypeptide(D) | Mass: 749.943 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: Fucosylated D-antimicrobial peptide SB4, incompletely resolved structure. Full sequence: (DLY)(DTY)(DLY)(DLY)(DAL)(DLE)(DLY)(DLY)(DLE)(DAL)(DLY)(DLE)(DLE) Source: (synth.) synthetic construct (others) |
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-Protein / Sugars , 2 types, 8 molecules ABCD
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 4 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 #5: Sugar | ChemComp-ZDC / |
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-Non-polymers , 3 types, 344 molecules
#4: Chemical | ChemComp-CA / #6: Chemical | #7: 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: 2.35 Å3/Da / Density % sol: 47.62 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 0.1 M Sodium chloride, 0.1 M BICINE pH 9.0, 20% v/v Polyethylene glycol monomethyl ether 550 |
-Data collection
Diffraction | Mean temperature: 80 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 16, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.009→41.629 Å / Num. all: 31842 / Num. obs: 31842 / % possible obs: 99.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.042 / Rrim(I) all: 0.078 / Rsym value: 0.066 / Net I/av σ(I): 9.5 / Net I/σ(I): 12.4 / Num. measured all: 107976 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-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 / Resolution: 2.009→41.629 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.28 / Phase error: 25.45 / 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: 127.16 Å2 / Biso mean: 38.007 Å2 / Biso min: 17.18 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.009→41.629 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: 22
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