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Open data
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Basic information
Entry | Database: PDB / ID: 4du0 | ||||||
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Title | Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) | ||||||
![]() | Neutrophil defensin 1 | ||||||
![]() | ANTIBIOTIC / cysteine rich antimicrobial peptide / alpha-defensin / HNP1 / human alpha-defensin 1 / G17A mutant / defensin fold / antimicrobial peptide / human neutrophils | ||||||
Function / homology | ![]() pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to virus / defense response to Gram-negative bacterium / collagen-containing extracellular matrix / killing of cells of another organism / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Wu, X. / Lu, W. / Pazgier, M. | ||||||
![]() | ![]() Title: Invariant gly residue is important for alpha-defensin folding, dimerization, and function: a case study of the human neutrophil alpha-defensin HNP1 Authors: Zhao, L. / Ericksen, B. / Wu, X. / Zhan, C. / Yuan, W. / Li, X. / Pazgier, M. / Lu, W. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 64.6 KB | Display | ![]() |
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PDB format | ![]() | 50.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 433.5 KB | Display | ![]() |
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Full document | ![]() | 433.7 KB | Display | |
Data in XML | ![]() | 8.2 KB | Display | |
Data in CIF | ![]() | 11 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1gnyS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein/peptide | Mass: 3466.137 Da / Num. of mol.: 4 / Fragment: UNP residues 65-94 / Mutation: G81A / Source method: obtained synthetically / Source: (synth.) ![]() #2: Chemical | ChemComp-GOL / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.74 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2012 |
Radiation | Monochromator: side scattering I-beam bend single crystal, asymmetric cut 4.9650 deg Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 12600 / Num. obs: 12600 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.144 / Rsym value: 0.107 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.9→1.93 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.859 / Mean I/σ(I) obs: 2.5 / Num. unique all: 625 / Rsym value: 0.981 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 1GNY Resolution: 1.9→42.28 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.885 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.128 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.804 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→42.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.898→1.947 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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