+Open data
-Basic information
Entry | Database: PDB / ID: 5nmn | ||||||
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Title | Atomic resolution structure of LL-37 in a monomeric state | ||||||
Components | Cathelicidin antimicrobial peptide | ||||||
Keywords | ANTIMICROBIAL PROTEIN / antimicrobial peptide / cathelicidin / LL-37 / atomic resolution | ||||||
Function / homology | Function and homology information cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection ...cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection / lipopolysaccharide binding / specific granule lumen / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / cellular response to tumor necrosis factor / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.95 Å | ||||||
Authors | Zeth, K. / Sancho-Vaello, E. | ||||||
Citation | Journal: Sci Rep / Year: 2017 Title: Structural remodeling and oligomerization of human cathelicidin on membranes suggest fibril-like structures as active species. Authors: Sancho-Vaello, E. / Francois, P. / Bonetti, E.J. / Lilie, H. / Finger, S. / Gil-Ortiz, F. / Gil-Carton, D. / Zeth, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nmn.cif.gz | 32.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nmn.ent.gz | 25.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nmn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nm/5nmn ftp://data.pdbj.org/pub/pdb/validation_reports/nm/5nmn | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4504.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913 |
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#2: Chemical | ChemComp-NA / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.33 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: PEG3350, 100 mM Tris, pH 8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 0.95→50 Å / Num. obs: 99140 / % possible obs: 92.6 % / Redundancy: 4.75 % / CC1/2: 0.999 / Net I/σ(I): 16.18 |
Reflection shell | Resolution: 0.95→1.01 Å / Mean I/σ(I) obs: 1.36 / Num. unique obs: 2853 / CC1/2: 0.917 / Rrim(I) all: 1.125 / % possible all: 79.2 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO PHASING / Resolution: 0.95→29.136 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.13
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.95→29.136 Å
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Refine LS restraints |
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LS refinement shell |
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