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Open data
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Basic information
Entry | Database: PDB / ID: 2nlf | ||||||
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Title | Human beta-defensin-1 (Mutant Leu13Glu) | ||||||
![]() | Beta-defensin 1 | ||||||
![]() | ANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin / mutant | ||||||
Function / homology | ![]() positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / sperm midpiece / innate immune response in mucosa / response to bacterium / calcium-mediated signaling / Golgi lumen ...positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / sperm midpiece / innate immune response in mucosa / response to bacterium / calcium-mediated signaling / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / innate immune response / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Lubkowski, J. / Pazgier, M. | ||||||
![]() | ![]() Title: Studies of the Biological Properties of Human beta-Defensin 1. Authors: Pazgier, M. / Prahl, A. / Hoover, D.M. / Lubkowski, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 52.8 KB | Display | ![]() |
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PDB format | ![]() | 38 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2nlbC ![]() 2nlcC ![]() 2nldC ![]() 2nleC ![]() 2nlgC ![]() 2nlhC ![]() 2nlpC ![]() 2nlqC ![]() 2nlsC ![]() 1ijvS 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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1 | ![]()
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3 | ![]()
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7 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | Biological assembly is a monomer |
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Components
#1: Protein/peptide | Mass: 3956.554 Da / Num. of mol.: 2 / Fragment: Human beta-defensin 1, residues 33-68 / Mutation: L13E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.04 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 10, 2004 / Details: osmic mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.45→40 Å / Num. all: 13851 / Num. obs: 13851 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Χ2: 0.977 / Net I/σ(I): 18 |
Reflection shell | Resolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1365 / Χ2: 0.956 / % possible all: 97.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1IJV Resolution: 1.45→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.051 / SU ML: 0.037 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / ESU R Free: 0.07 / Stereochemistry target values: Engh & Huber
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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 mean: 13.457 Å2
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Refinement step | Cycle: LAST / Resolution: 1.45→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.488 Å / Total num. of bins used: 20
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