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Open data
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Basic information
Entry | Database: PDB / ID: 1iju | ||||||
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Title | HUMAN BETA-DEFENSIN-1 | ||||||
![]() | BETA-DEFENSIN 1 | ||||||
![]() | ANTIBIOTIC / DEFENSIN / HUMAN BETA-DEFENSIN-1 / BETA-DEFENSIN | ||||||
Function / homology | ![]() positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium ...positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / 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 | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hoover, D.M. / Lubkowski, J. | ||||||
![]() | ![]() Title: The structure of human beta-defensin-1: new insights into structural properties of beta-defensins. Authors: Hoover, D.M. / Chertov, O. / 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 | ![]() | 49.9 KB | Display | ![]() |
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PDB format | ![]() | 36.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 476.5 KB | Display | ![]() |
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Full document | ![]() | 478.5 KB | Display | |
Data in XML | ![]() | 12.1 KB | Display | |
Data in CIF | ![]() | 17.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related 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: 3940.598 Da / Num. of mol.: 4 / Source method: obtained synthetically Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS). References: UniProt: P60022 #2: Chemical | ChemComp-SO4 / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.77 Å3/Da / Density % sol: 30.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: PEG 4000, ammonium sulfate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||
Detector | Type: ADSC / Detector: CCD / Date: Mar 4, 2001 / Details: MIRRORS | |||||||||
Radiation | Monochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 1.4→20 Å / Num. all: 87587 / Num. obs: 26325 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 27.2 | |||||||||
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / % possible all: 64.1 | |||||||||
Reflection | *PLUS Highest resolution: 1.4 Å / Num. measured all: 87587 | |||||||||
Reflection shell | *PLUS % possible obs: 64.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: HUMAN BETA-DEFENSIN-1 Resolution: 1.4→20 Å / Num. parameters: 6199 / Num. restraintsaints: 5551 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 1040 / Occupancy sum non hydrogen: 1350 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.4→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 4.4 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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