+Open data
-Basic information
Entry | Database: PDB / ID: 1fd4 | ||||||
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Title | HUMAN BETA-DEFENSIN 2 | ||||||
Components | BETA-DEFENSIN 2 | ||||||
Keywords | ANTIMICROBIAL PEPTIDE / 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 / MOLECULAR REPLACEMENT / Resolution: 1.7 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fd4.cif.gz | 149.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fd4.ent.gz | 120.6 KB | Display | PDB format |
PDBx/mmJSON format | 1fd4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fd/1fd4 ftp://data.pdbj.org/pub/pdb/validation_reports/fd/1fd4 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | The biological assembly is a dimer. |
-Components
#1: Protein/peptide | Mass: 4342.271 Da / Num. of mol.: 16 / 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1 Å3/Da / Density % sol: 45.21 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG 4000, tris, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: used macroseeding | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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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: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 65644 / Num. obs: 65644 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.7 / % possible all: 96.3 |
Reflection | *PLUS % possible obs: 97.1 % / Num. measured all: 165583 |
Reflection shell | *PLUS % possible obs: 96.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HUMAN BETA-DEFESIN-2 Resolution: 1.7→30 Å / Num. parameters: 2327 / Num. restraintsaints: 2138 / 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: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5615 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→30 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: 11 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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