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Open data
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Basic information
Entry | Database: PDB / ID: 4mgp | ||||||
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Title | Structure of racemic Ala-(8,13,18) Magainin 2 | ||||||
![]() | Magainin 2 Derivative | ||||||
![]() | ANTIMICROBIAL PROTEIN / phenylalanine zipper | ||||||
Function / homology | regulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / Magainins![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hayouka, Z. / Mortenson, D.E. / Kreitler, D.F. / Weisblum, B. / Gellman, S.H. / Forest, K.T. | ||||||
![]() | ![]() Title: Evidence for Phenylalanine Zipper-Mediated Dimerization in the X-ray Crystal Structure of a Magainin 2 Analogue. Authors: Hayouka, Z. / Mortenson, D.E. / Kreitler, D.F. / Weisblum, B. / Forest, K.T. / Gellman, S.H. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 14.7 KB | Display | ![]() |
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PDB format | ![]() | 8.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 369.2 KB | Display | ![]() |
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Full document | ![]() | 369.1 KB | Display | |
Data in XML | ![]() | 1.9 KB | Display | |
Data in CIF | ![]() | 2.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2magS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein/peptide | Mass: 2483.989 Da / Num. of mol.: 1 / Fragment: UNP residues 83-105 / Mutation: S8A, G13A, G18A / Source method: obtained synthetically / Source: (synth.) ![]() |
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#2: Water | ChemComp-HOH / |
Sequence details | THESE RESIDUES ARE MODIFIED TO ALANINE. |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Precipitant solution contained 0.1 M sodium citrate tribasic, pH 5.6, and 35% v/v tert-butanol. No additional cryoprotectant was necessary for vitrification of crystals in LN2, VAPOR ...Details: Precipitant solution contained 0.1 M sodium citrate tribasic, pH 5.6, and 35% v/v tert-butanol. No additional cryoprotectant was necessary for vitrification of crystals in LN2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9786 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.75→26.72 Å / Num. obs: 2247 / % possible obs: 95.4 % / Redundancy: 22.4 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 32.17 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2MAG Resolution: 1.75→26.69 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.2748 / WRfactor Rwork: 0.2232 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.6576 / SU B: 3.415 / SU ML: 0.086 / SU R Cruickshank DPI: 0.1255 / SU Rfree: 0.1213 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.78 Å2 / Biso mean: 31.59 Å2 / Biso min: 17.49 Å2
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Refine analyze | Luzzati coordinate error obs: 0.086 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→26.69 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.844 Å / Total num. of bins used: 10
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