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Yorodumi- PDB-1zmk: Crystal structure of human alpha-defensin-2 (variant Gly16-> D-AL... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1zmk | ||||||
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Title | Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group | ||||||
Components | Neutrophil defensin 2 | ||||||
Keywords | ANTIMICROBIAL PROTEIN / alpha-defensin / antimicrobial / D-amino acid substitutions | ||||||
Function / homology | Function and homology information Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response ...Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / intracellular estrogen receptor signaling pathway / defense response to fungus / innate immune response in mucosa / Golgi lumen / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / 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 / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Lubkowski, J. / Prahl, A. / Lu, W. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2005 Title: Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids. Authors: Xie, C. / Prahl, A. / Ericksen, B. / Wu, Z. / Zeng, P. / Li, X. / Lu, W.Y. / Lubkowski, J. / Lu, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1zmk.cif.gz | 40.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1zmk.ent.gz | 29.1 KB | Display | PDB format |
PDBx/mmJSON format | 1zmk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zm/1zmk ftp://data.pdbj.org/pub/pdb/validation_reports/zm/1zmk | HTTPS FTP |
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-Related structure data
Related structure data | 1zmhC 1zmiC 1dfnS 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein/peptide | Mass: 3395.059 Da / Num. of mol.: 2 / Mutation: G16(DAL) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DEFA3, DEF3 / Production host: Escherichia coli (E. coli) / References: UniProt: P59666 #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: 2.07 Å3/Da / Density % sol: 40.65 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: tri-sodium citrate dihydrate, Tris/HCl, PEG 8000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.92 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 10, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→30 Å / Num. all: 24405 / Num. obs: 24405 / % possible obs: 97.7 % / Redundancy: 10.2 % / Rsym value: 0.07 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.1→1.15 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.429 / % possible all: 89.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Based on monomer of HNP-3 (PDB ID code 1DFN) Resolution: 1.3→19.47 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.27 / SU ML: 0.025 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.779 Å2
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Refinement step | Cycle: LAST / Resolution: 1.3→19.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.3→1.37 Å / Total num. of bins used: 10
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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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