+Open data
-Basic information
Entry | Database: PDB / ID: 1fd3 | ||||||
---|---|---|---|---|---|---|---|
Title | HUMAN BETA-DEFENSIN 2 | ||||||
Components | BETA-DEFENSIN 2 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / DEFENSIN / HUMAN BETA-DEFENSIN 2 / BETA-DEFENSIN | ||||||
Function / homology | Function and homology information CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis ...CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region Similarity search - Function | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å | ||||||
Authors | Hoover, D.M. / Lubkowski, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: The structure of human beta-defensin-2 shows evidence of higher order oligomerization. Authors: Hoover, D.M. / Rajashankar, K.R. / Blumenthal, R. / Puri, A. / Oppenheim, J.J. / Chertov, O. / Lubkowski, J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1fd3.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1fd3.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 1fd3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fd3 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fd3 | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer. |
-Components
#1: Protein/peptide | Mass: 4342.271 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: O15263 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 41.81 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, tris HCl, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: used macroseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979 |
Detector | Type: ADSC / Detector: CCD / Date: Oct 2, 1999 / Details: MIRRORS |
Radiation | Monochromator: SI CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→30 Å / Num. all: 28662 / Num. obs: 28662 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 55 |
Reflection shell | Resolution: 1.35→1.4 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 6.5 / % possible all: 90.1 |
Reflection | *PLUS Num. obs: 32227 / Num. measured all: 137572 |
Reflection shell | *PLUS % possible obs: 90.1 % |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MAD / Resolution: 1.35→30 Å / Num. parameters: 1274 / Num. restraintsaints: 1449 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
| |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 1 / Occupancy sum hydrogen: 1292 / Occupancy sum non hydrogen: 1411 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→30 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 11 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|