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Yorodumi- PDB-7new: Fucosylated heterochiral linear peptide Fdln69 bound to the fucos... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7new | |||||||||
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Title | Fucosylated heterochiral linear peptide Fdln69 bound to the fucose binding lectin LecB PA-IIL from Pseudomonas aeruginosa at 2.0 Angstrom resolution | |||||||||
Components |
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Keywords | ANTIBIOTIC / Antimicrobial peptide / Lectin / ANTIMICROBIAL PROTEIN | |||||||||
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: 2.02 Å | |||||||||
Authors | Personne, H. / Baeriswyl, S. / Stocker, A. / Reymond, J.-L. | |||||||||
Funding support | Switzerland, 1items
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Citation | Journal: Rsc Chem Biol / Year: 2021 Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L. #1: Journal: Rsc Chem Biol / Year: 2021 Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L. #2: Journal: Rsc Chem Biol / Year: 2021 Title: A mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography. Authors: Baeriswyl, S. / Personne, H. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / Reymond, J.L. #3: Journal: Chemrxiv / Year: 2021 Title: Mixed chirality alpha-helix in a stapled bicyclic and a linear antimicrobial peptide revealed by X-ray crystallography Authors: Personne, H. / Baeriswyl, S. / Di Bonaventura, I. / Kohler, T. / van Delden, C. / Stocker, A. / Javor, S. / 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 | 7new.cif.gz | 195.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7new.ent.gz | 154.8 KB | Display | PDB format |
PDBx/mmJSON format | 7new.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7new_validation.pdf.gz | 497.8 KB | Display | wwPDB validaton report |
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Full document | 7new_full_validation.pdf.gz | 501.2 KB | Display | |
Data in XML | 7new_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 7new_validation.cif.gz | 30.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/7new ftp://data.pdbj.org/pub/pdb/validation_reports/ne/7new | HTTPS FTP |
-Related structure data
Related structure data | 6y0uC 6y0vC 6y13C 6y14C 6y1sC 7nefC 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 11865.905 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Fucose-binding Lectin LecB PA-IIL from Pseudomonas aeruginosa Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: lecB, C0044_25260, CAZ10_21840, DT376_00595, DY979_15445, ECC04_10105, EFK27_13700, EGV95_09240, EGY23_15550, IPC669_23070, PA5486_01888, PAERUG_E15_London_28_01_14_00983, PAMH19_1713, RW109_RW109_02453 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS #2: Polypeptide(D) | Mass: 1324.847 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Fucosylated heterochiral linear peptide Fdln69 / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-CA / #4: Sugar | ChemComp-ZDC / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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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: 2.81 Å3/Da / Density % sol: 56.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.2M Sodium citrate tribasic dihydrate, 0.1M Sodium cacodylate trihydrate pH 6.5, 30% v/v 2-Propanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.976437 Å |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 2, 2020 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976437 Å / Relative weight: 1 |
Reflection | Resolution: 2.017→48.288 Å / Num. obs: 71291 / % possible obs: 97.5 % / Redundancy: 3.55 % / CC1/2: 0.995 / Rrim(I) all: 0.167 / Net I/σ(I): 6.89 |
Reflection shell | Resolution: 2.02→2.14 Å / Redundancy: 3.48 % / Mean I/σ(I) obs: 1.01 / Num. unique obs: 11367 / CC1/2: 0.512 / % possible all: 96.1 |
-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: 2.02→40.03 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 27.17 / 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: 161.23 Å2 / Biso mean: 43.0425 Å2 / Biso min: 25.46 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.02→40.03 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Origin x: 26.2953 Å / Origin y: 8.6788 Å / Origin z: 17.1692 Å
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Refinement TLS group |
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