+Open data
-Basic information
Entry | Database: PDB / ID: 5ngq | ||||||
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Title | Bicyclic antimicrobial peptides | ||||||
Components |
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Keywords | SUGAR BINDING PROTEIN / Bycicle / Antimicrobial peptide / Pseudomonas aeruginosa / Biofilm | ||||||
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: 1.17 Å | ||||||
Authors | Di Bonaventura, I. / Jin, X. / Visini, R. / Michaud, G. / Robadey, M. / Koehler, T. / van Delden, C. / Stocker, A. / Darbre, T. / Reymond, J.-L. | ||||||
Citation | Journal: Chem Sci / Year: 2017 Title: Chemical space guided discovery of antimicrobial bridged bicyclic peptides against Pseudomonas aeruginosa and its biofilms. Authors: Di Bonaventura, I. / Jin, X. / Visini, R. / Probst, D. / Javor, S. / Gan, B.H. / Michaud, G. / Natalello, A. / Doglia, S.M. / Kohler, T. / van Delden, C. / 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 | 5ngq.cif.gz | 201.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5ngq.ent.gz | 162.4 KB | Display | PDB format |
PDBx/mmJSON format | 5ngq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5ngq_validation.pdf.gz | 477.8 KB | Display | wwPDB validaton report |
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Full document | 5ngq_full_validation.pdf.gz | 479.6 KB | Display | |
Data in XML | 5ngq_validation.xml.gz | 23.2 KB | Display | |
Data in CIF | 5ngq_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ng/5ngq ftp://data.pdbj.org/pub/pdb/validation_reports/ng/5ngq | HTTPS FTP |
-Related structure data
Related structure data | 5i8mC 5i8xC 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/peptide , 2 types, 4 molecules EFGH
#2: Protein/peptide | Mass: 1039.248 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#3: Protein/peptide | Mass: 534.734 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-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 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 #5: Sugar | ChemComp-ZDC / |
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-Non-polymers , 2 types, 464 molecules
#4: Chemical | ChemComp-CA / #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: 1.93 Å3/Da / Density % sol: 36.29 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop Details: 0.1 M sodium acetate trihydrate pH 4.6 and 2.0 M ammonium sulfate. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.99999 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 7, 2015 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99999 Å / Relative weight: 1 |
Reflection | Resolution: 1.17→47.226 Å / Num. obs: 125097 / % possible obs: 97.2 % / Redundancy: 3.1 % / Rrim(I) all: 0.038 / Net I/σ(I): 17.74 |
Reflection shell | Resolution: 1.17→1.24 Å / Mean I/σ(I) obs: 3.06 / Num. measured obs: 49037 / Num. unique all: 18095 / CC1/2: 0.907 / Rrim(I) all: 0.359 / % possible all: 87.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1OXC Resolution: 1.17→47.23 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.13 / Phase error: 15.43
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.17→47.23 Å
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Refine LS restraints |
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LS refinement shell |
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