+Open data
-Basic information
Entry | Database: PDB / ID: 3qte | ||||||
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Title | Crystal structure of human alpha-defensin 6 (H27W mutant) | ||||||
Components | Defensin-6 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / Paneth cells defensin / HD6 / human alpha defensin | ||||||
Function / homology | Function and homology information Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide ...Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / protein homodimerization activity / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.949 Å | ||||||
Authors | Pazgier, M. / Lu, W. | ||||||
Citation | Journal: Science / Year: 2012 Title: Human alpha-defensin 6 promotes mucosal innate immunity through self-assembled peptide nanonets. Authors: Chu, H. / Pazgier, M. / Jung, G. / Nuccio, S.P. / Castillo, P.A. / de Jong, M.F. / Winter, M.G. / Winter, S.E. / Wehkamp, J. / Shen, B. / Salzman, N.H. / Underwood, M.A. / Tsolis, R.M. / ...Authors: Chu, H. / Pazgier, M. / Jung, G. / Nuccio, S.P. / Castillo, P.A. / de Jong, M.F. / Winter, M.G. / Winter, S.E. / Wehkamp, J. / Shen, B. / Salzman, N.H. / Underwood, M.A. / Tsolis, R.M. / Young, G.M. / Lu, W. / Lehrer, R.I. / Baumler, A.J. / Bevins, C.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3qte.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3qte.ent.gz | 50 KB | Display | PDB format |
PDBx/mmJSON format | 3qte.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qt/3qte ftp://data.pdbj.org/pub/pdb/validation_reports/qt/3qte | HTTPS FTP |
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-Related structure data
Related structure data | 1zmqS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 3767.367 Da / Num. of mol.: 4 / Fragment: Processed peptide (UNP Residues 69-100) / Mutation: H95W / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01524 #2: Chemical | #3: Chemical | ChemComp-GOL / | #4: 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: 1.88 Å3/Da / Density % sol: 34.47 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1 M imidazole, pH 6.5, 1M Na acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-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: Apr 24, 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: 1.949→50 Å / Num. all: 8330 / Num. obs: 8258 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.105 / Rsym value: 0.088 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 1.949→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.504 / % possible all: 92 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZMQ Resolution: 1.949→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.611 / SU ML: 0.101 / SU R Cruickshank DPI: 0.0449 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.237 Å2
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Refinement step | Cycle: LAST / Resolution: 1.949→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.949→2 Å / Total num. of bins used: 20
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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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