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- PDB-1zmh: Crystal structure of human neutrophil peptide 2, HNP-2 (variant G... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1zmh | ||||||
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Title | Crystal structure of human neutrophil peptide 2, HNP-2 (variant Gly16-> D-Ala) | ||||||
![]() | Neutrophil defensin 2 | ||||||
![]() | ANTIMICROBIAL PROTEIN / alpha-defensin / D-amino acid substitution | ||||||
Function / homology | ![]() Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response ...Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to virus / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Lubkowski, J. / Prahl, A. / Lu, W. | ||||||
![]() | ![]() Title: Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. Authors: Xie, C. / Prahl, A. / Ericksen, B. / Wu, Z. / Zeng, P. / Li, X. / Lu, W.Y. / Lubkowski, J. / 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 | ![]() | 67 KB | Display | ![]() |
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PDB format | ![]() | 51 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1zmiC ![]() 1zmkC ![]() 1defS C: citing same article ( 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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4 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 3395.059 Da / Num. of mol.: 4 / Mutation: G16(DAL) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-P6G / | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.53 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: lithium sulfate, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.48→50 Å / Num. all: 20719 / Num. obs: 20719 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038 |
Reflection shell | Resolution: 1.48→1.55 Å / % possible all: 65.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: BASED ON MONOMER OF HNP-3 (PDB ENTRY 1DEF) Resolution: 1.5→19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.676 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 26.748 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→19 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.581 Å / Total num. of bins used: 10
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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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