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Yorodumi- PDB-5ney: Discovery, crystal structures and atomic force microscopy study o... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5ney | |||||||||
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Title | Discovery, crystal structures and atomic force microscopy study of thioether ligated D,L-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa | |||||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / Cyclic peptides / Antimicrobials / Pseudomonas aeruginosa | |||||||||
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 / Resolution: 1.55 Å | |||||||||
Authors | Reymond, J.-L. / Darbre, T. / Stocker, A. / Hong, W. / van Delden, C. / Koehler, T. / Luscher, A. / Visini, R. / Fu, Y. / Di Bonaventura, I. / He, R. | |||||||||
Citation | Journal: Chem Sci / Year: 2017 Title: Design, crystal structure and atomic force microscopy study of thioether ligated d,l-cyclic antimicrobial peptides against multidrug resistant Pseudomonas aeruginosa. Authors: He, R. / Di Bonaventura, I. / Visini, R. / Gan, B.H. / Fu, Y. / Probst, D. / Luscher, A. / Kohler, T. / van Delden, C. / Stocker, A. / Hong, W. / 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 | 5ney.cif.gz | 111.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ney.ent.gz | 84.2 KB | Display | PDB format |
PDBx/mmJSON format | 5ney.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ney_validation.pdf.gz | 485.5 KB | Display | wwPDB validaton report |
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Full document | 5ney_full_validation.pdf.gz | 490.1 KB | Display | |
Data in XML | 5ney_validation.xml.gz | 23.9 KB | Display | |
Data in CIF | 5ney_validation.cif.gz | 34.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ne/5ney ftp://data.pdbj.org/pub/pdb/validation_reports/ne/5ney | HTTPS FTP |
-Related structure data
Related structure data | 5nesC 5nf0C 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 / Protein/peptide / Sugars , 3 types, 9 molecules ABCDE
#1: Protein | Mass: 11734.707 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: lecB, PAERUG_E15_London_28_01_14_00983, PAERUG_P32_London_17_VIM_2_10_11_00423, PAMH19_1713 Production host: Escherichia coli (E. coli) / References: UniProt: A0A069Q9V4, UniProt: Q9HYN5*PLUS #2: Protein/peptide | | Mass: 1683.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Sugar | ChemComp-ZDC / |
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-Non-polymers , 3 types, 402 molecules
#4: Chemical | ChemComp-CA / #5: Chemical | ChemComp-OXE / | #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: 2.1 Å3/Da / Density % sol: 41.48 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.5 M Ammonium Sulfate, 0.1M Sodium citrate tribasic dehydrate, 1.0 M Lithium sulfate monohydrate, pH 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 29, 2016 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 1.55→47.43 Å / Num. obs: 53265 / % possible obs: 89.6 % / Redundancy: 2.23 % / Rrim(I) all: 0.07 / Net I/σ(I): 12.44 |
Reflection shell | Resolution: 1.55→1.64 Å / Mean I/σ(I) obs: 2.58 / Num. unique all: 8356 / CC1/2: 0.754 / Rrim(I) all: 0.532 / % possible all: 87.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OXC Resolution: 1.55→47.428 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.3 / Phase error: 23.02
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.55→47.428 Å
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Refine LS restraints |
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LS refinement shell |
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