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Yorodumi- PDB-4lb1: Crystal structure of human alpha-defensin 1 (HNP1) Y16A/F28A mutant -
+Open data
-Basic information
Entry | Database: PDB / ID: 4lb1 | ||||||
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Title | Crystal structure of human alpha-defensin 1 (HNP1) Y16A/F28A mutant | ||||||
Components | Neutrophil defensin 1 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / HUMAN ALPHA DEFENSIN 1 / HUMAN NEUTROPHIL PEPTIDE 1 / HNP1 / ANTIBIOTIC / ANTIMICROBIAL / ANTIVIRAL DEFENSE / DEFENSIN / DISULFIDE BOND / FUNGICIDE / PHOSPHOPROTEIN / SECRETED | ||||||
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 / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Tolbert, W.D. / Wu, X. / Pazgier, M. | ||||||
Citation | Journal: Plos One / Year: 2013 Title: Single, Double and Quadruple Alanine Substitutions at Oligomeric Interfaces Identify Hydrophobicity as the Key Determinant of Human Neutrophil Alpha Defensin HNP1 Function. Authors: Zhao, L. / Tolbert, W.D. / Ericksen, B. / Zhan, C. / Wu, X. / Yuan, W. / Li, X. / Pazgier, M. / Lu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lb1.cif.gz | 55.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lb1.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lb1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/4lb1 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/4lb1 | HTTPS FTP |
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-Related structure data
Related structure data | 4lb7C 4lbbC 4lbfC 3gnyS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3283.919 Da / Num. of mol.: 4 / Mutation: Y16A, F28A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665 #2: 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: 3.11 Å3/Da / Density % sol: 60.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 2 M ammonium phosphate monobasic, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.979 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 11, 2012 / Details: RH COATED FLAT MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 10725 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 21.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 1.3 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3GNY Resolution: 2→18.037 Å / SU ML: 0.22 / σ(F): 1.98 / Phase error: 26.35 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→18.037 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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