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Yorodumi- PDB-1dfn: CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHAN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dfn | ||||||
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Title | CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION | ||||||
Components | DEFENSIN HNP-3 | ||||||
Keywords | DEFENSIN | ||||||
Function / homology | Function and homology information pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / collagen-containing extracellular matrix / defense response to virus / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.9 Å | ||||||
Authors | Hill, C.P. / Yee, J. / Selsted, M.E. / Eisenberg, D. | ||||||
Citation | Journal: Science / Year: 1991 Title: Crystal structure of defensin HNP-3, an amphiphilic dimer: mechanisms of membrane permeabilization. Authors: Hill, C.P. / Yee, J. / Selsted, M.E. / Eisenberg, D. #1: Journal: J.Clin.Invest. / Year: 1985 Title: Primary Structures of Three Human Neutrophil Defensins Authors: Selsted, M.E. / Harwig, S.S.L. / Ganz, T. / Schilling, J.W. / Lehrer, R.I. #2: Journal: J.Clin.Invest. / Year: 1985 Title: Defensins. Natural Peptide Antibiotics of Human Neutrophils Authors: Ganz, T. / Selsted, M.E. / Szklarek, D. / Harwig, S.S.L. / Daher, K. / Bainton, D.F. / Lehrer, R.I. | ||||||
History |
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Remark 700 | SHEET THERE IS A CLASSIC BULGE INVOLVING RESIDUES 17, 18, AND 29 FOR EACH OF THE CHAINS. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dfn.cif.gz | 20.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dfn.ent.gz | 15.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dfn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/df/1dfn ftp://data.pdbj.org/pub/pdb/validation_reports/df/1dfn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Atom site foot note | 1: RESIDUES A 8 AND B 8 ARE CIS PROLINES. 2: THERE IS A CLASSIC BULGE INVOLVING RESIDUES 17, 18, AND 29 FOR EACH OF THE CHAINS. | ||||||||
Components on special symmetry positions |
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Details | THE TWO MOLECULES IN THE ASYMMETRIC UNIT HAVE BEEN ASSIGNED CHAIN IDENTIFIERS *A* AND *B*. EACH OF THE TWO MONOMERS IN THE ASYMMETRIC UNIT CONTAINS A THREE STRAND ANTIPARALLEL SHEET. A LOCAL TWO-FOLD AXIS RELATING MOLECULES *A* AND *B* RESULTS IN A SIX-STRANDED ANTIPARALLEL SHEET IN THE DIMER. THE TWO MOLECULES IN THE ASYMMETRIC UNIT ARE RELATED TO EACH OTHER BY A LOCAL TWO-FOLD AXIS. |
-Components
#1: Protein/peptide | Mass: 3496.121 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P59665, UniProt: P59666*PLUS #2: Water | ChemComp-HOH / | Sequence details | THE 30 RESIDUES IN HNP-3 HAVE BEEN NUMBERED FROM 2 - 31 IN ORDER TO BETTER FIT THE SEQUENCE ...THE 30 RESIDUES IN HNP-3 HAVE BEEN NUMBERED FROM 2 - 31 IN ORDER TO BETTER FIT THE SEQUENCE ALIGNMENT WITH OTHER DEFENSIN MOLECULES. | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.39 % | ||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 4 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 1.9 Å / Num. obs: 4524 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Num. measured all: 22975 / Rmerge F obs: 0.054 / Biso Wilson estimate: 15.6 Å2 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 1.9→10 Å / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.9 Å / Lowest resolution: 10 Å / Num. reflection all: 4448 / Rfactor obs: 0.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |