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- PDB-4mgp: Structure of racemic Ala-(8,13,18) Magainin 2 -

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Basic information

Entry
Database: PDB / ID: 4mgp
TitleStructure of racemic Ala-(8,13,18) Magainin 2
ComponentsMagainin 2 Derivative
KeywordsANTIMICROBIAL PROTEIN / phenylalanine zipper
Function / homologyantimicrobial peptide biosynthetic process / extraorganismal space / regulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / Magainins
Function and homology information
Biological speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsHayouka, Z. / Mortenson, D.E. / Kreitler, D.F. / Weisblum, B. / Gellman, S.H. / Forest, K.T.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
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
DepositionAug 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2013Group: Database references
Revision 1.2Nov 6, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Magainin 2 Derivative


Theoretical massNumber of molelcules
Total (without water)2,4841
Polymers2,4841
Non-polymers00
Water905
1
A: Magainin 2 Derivative

A: Magainin 2 Derivative


Theoretical massNumber of molelcules
Total (without water)4,9682
Polymers4,9682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)53.380, 53.459, 29.750
Angle α, β, γ (deg.)89.970, 90.070, 89.980
Int Tables number122
Space group name H-MI-42d
Components on special symmetry positions
IDModelComponents
11A-101-

HOH

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Components

#1: Protein/peptide Magainin 2 Derivative


Mass: 2483.989 Da / Num. of mol.: 1 / Fragment: UNP residues 83-105 / Mutation: S8A, G13A, G18A / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog) / References: UniProt: P11006
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHESE RESIDUES ARE MODIFIED TO ALANINE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 23, 2013
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 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
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
1.75-1.794.80.3743.974164.3
1.79-1.847.850.3034.64128176.2
1.84-1.8911.390.2687.96133185.8
1.89-1.9417.740.24312.39139199.3
1.94-1.9923.420.23115.061211100
1.99-2.0425.450.18718.87117199.2
2.04-2.126.980.16625.371231100
2.1-2.1727.350.13528.811291100
2.17-2.2527.630.1230.861251100
2.25-2.3427.910.11140.811211100
2.34-2.4427.420.11243.71191100
2.44-2.5527.280.10342.231131100
2.55-2.727.860.09646.521181100
2.7-2.8927.550.08251.51171100
2.89-3.1226.80.08749.941141100
3.12-3.4626.710.08554.721151100
3.46-4.0125.730.08852.551141100
4.01-5.1124.610.07846.581131100
5.11-26.7220.760.09137.11114197.4

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Processing

Software
NameVersionClassificationNB
XPREP2008/2 for Windowsdata reduction
REFMACrefinement
PDB_EXTRACT3.11data extraction
EMBLMD-2data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2MAG

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
RfactorNum. reflection% reflectionSelection details
Rfree0.2328 95 4.4 %RANDOM
Rwork0.1965 ---
obs0.1983 2169 95.42 %-
all-2169 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.78 Å2 / Biso mean: 31.59 Å2 / Biso min: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20 Å2-0 Å2
2---0.63 Å20 Å2
3---1.27 Å2
Refine analyzeLuzzati coordinate error obs: 0.086 Å
Refinement stepCycle: LAST / Resolution: 1.75→26.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms163 0 0 5 168
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.019172
X-RAY DIFFRACTIONr_bond_other_d0.0010.02176
X-RAY DIFFRACTIONr_angle_refined_deg2.431.915230
X-RAY DIFFRACTIONr_angle_other_deg1.1893400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.806523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.84823.3336
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.791530
X-RAY DIFFRACTIONr_chiral_restr0.1650.225
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02195
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0243
LS refinement shellResolution: 1.75→1.844 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.365 9 -
Rwork0.338 228 -
all-237 -
obs-228 73.37 %

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