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- PDB-4e83: Crystal structure of human alpha-defensin 5, HD5 (Leu29NLe mutant) -
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Open data
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Basic information
Entry | Database: PDB / ID: 4.0E+83 | ||||||
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Title | Crystal structure of human alpha-defensin 5, HD5 (Leu29NLe mutant) | ||||||
![]() | Defensin-5 | ||||||
![]() | ANTIMICROBIAL PROTEIN / beta-sheet structure / antimicrobial peptide / Leu29Nle mutant / Paneth cells | ||||||
Function / homology | ![]() positive regulation of membrane permeability / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / Alpha-defensins / defense response to fungus / transport vesicle / extracellular matrix / innate immune response in mucosa / secretory granule ...positive regulation of membrane permeability / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / Alpha-defensins / defense response to fungus / transport vesicle / extracellular matrix / innate immune response in mucosa / secretory granule / positive regulation of interleukin-8 production / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / midbody / antibacterial humoral response / cellular response to lipopolysaccharide / protein homotetramerization / secretory granule lumen / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / intracellular membrane-bounded organelle / innate immune response / protein homodimerization activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Pazgier, M. | ||||||
![]() | ![]() Title: Functional determinants of human enteric {alpha}-defensin HD5: crucial role for hydrophobicity at dimer interface. Authors: Rajabi, M. / Ericksen, B. / Wu, X. / de Leeuw, E. / Zhao, L. / 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 | ![]() | 37.4 KB | Display | ![]() |
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PDB format | ![]() | 26.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 427.5 KB | Display | ![]() |
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Full document | ![]() | 427.9 KB | Display | |
Data in XML | ![]() | 5.1 KB | Display | |
Data in CIF | ![]() | 6.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4e82C ![]() 4e86C ![]() 1zmpS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 32 / Label seq-ID: 1 - 32
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Components
#1: Protein/peptide | Mass: 3594.228 Da / Num. of mol.: 2 / Fragment: UNP residues 63-94 / Source method: obtained synthetically / Source: (synth.) ![]() #2: Chemical | ChemComp-CL / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.69 Å3/Da / Density % sol: 27.25 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.0 M HEPES sodium, pH 7.5, 0.2 M magnesium chloride hexahydrate, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 1, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.81→50 Å / Num. all: 8069 / Num. obs: 4623 / % possible obs: 57 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.081 / Rsym value: 0.057 / Net I/σ(I): 21 |
Reflection shell | Resolution: 1.81→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.362 / % possible all: 66.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ZMP Resolution: 1.9→32.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.897 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 96.34 Å2 / Biso mean: 51.818 Å2 / Biso min: 24.01 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→32.96 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 0.634 Å / Origin y: 11.456 Å / Origin z: -0.214 Å
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Refinement TLS group |
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