+Open data
-Basic information
Entry | Database: PDB / ID: 3loe | ||||||
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Title | Crystal structure of human alpha-defensin 1 (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 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.56 Å | ||||||
Authors | Pazgier, M. / Lu, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2010 Title: Trp-26 imparts functional versatility to human alpha-defensin HNP1. Authors: Wei, G. / Pazgier, M. / de Leeuw, E. / Rajabi, M. / Li, J. / Zou, G. / Jung, G. / Yuan, W. / Lu, W.Y. / Lehrer, R.I. / Lu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3loe.cif.gz | 18.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3loe.ent.gz | 10.9 KB | Display | PDB format |
PDBx/mmJSON format | 3loe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lo/3loe ftp://data.pdbj.org/pub/pdb/validation_reports/lo/3loe | HTTPS FTP |
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-Related structure data
Related structure data | 3h6cC 3lo1C 3lo2C 3lo4C 3lo6C 3lo9C 3lvxC 1gnyS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3376.015 Da / Num. of mol.: 1 / Fragment: UNP residues 65-94 / Mutation: F28A / Source method: obtained synthetically / Details: Protein naturally occurs in HUMAN / References: UniProt: P59665 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.81 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 25% PEG 4,000; 0.2 M ammonium sulfate; 0.1 M sodium acetate, pH 4.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 23, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.56→30.182 Å / Num. all: 4349 / Num. obs: 4342 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.103 / Net I/σ(I): 20.1 |
Reflection shell | Resolution: 1.56→1.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.098 / Mean I/σ(I) obs: 18.6 / Num. unique all: 167 / Rsym value: 0.116 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GNY Resolution: 1.56→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.585 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.076 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 49.56 Å2 / Biso mean: 17.603 Å2 / Biso min: 10.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.56→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.563→1.604 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -11.5045 Å / Origin y: -3.9118 Å / Origin z: -10.7205 Å
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Refinement TLS group |
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