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- PDB-5cgn: Structure of quasiracemic Ala-Magainin 2 with a beta amino acid s... -

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Basic information

Entry
Database: PDB / ID: 5cgn
TitleStructure of quasiracemic Ala-Magainin 2 with a beta amino acid substitution at position 8
Components
  • D-Ala-Magainin Derivative
  • L-ACPC8-Ala-Magainin
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial / quasiracemate / homochiral dimerization / beta amino acid
Function / homologyregulation of defense response to virus / defense response to fungus / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / polypeptide(D) / polypeptide(D) (> 10) / Magainins
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHayouka, Z. / Thomas, N.C. / Mortenson, D.E. / Satyshur, K.A. / Weisblum, B. / Forest, K.T. / Gellman, S.H.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM061238 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM08293 United States
National Science Foundation (NSF, United States)NSF DMR-832760 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM100346 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: Quasiracemate Crystal Structures of Magainin 2 Derivatives Support the Functional Significance of the Phenylalanine Zipper Motif.
Authors: Hayouka, Z. / Thomas, N.C. / Mortenson, D.E. / Satyshur, K.A. / Weisblum, B. / Forest, K.T. / Gellman, S.H.
History
DepositionJul 9, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2015Group: Database references
Revision 1.2Oct 7, 2015Group: Derived calculations
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 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
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-Ala-Magainin Derivative
B: D-Ala-Magainin Derivative
C: D-Ala-Magainin Derivative
D: D-Ala-Magainin Derivative
E: L-ACPC8-Ala-Magainin
F: L-ACPC8-Ala-Magainin
G: L-ACPC8-Ala-Magainin
H: L-ACPC8-Ala-Magainin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,14310
Polymers20,0728
Non-polymers712
Water55831
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-49 kcal/mol
Surface area13480 Å2
2
A: D-Ala-Magainin Derivative
B: D-Ala-Magainin Derivative
C: D-Ala-Magainin Derivative
D: D-Ala-Magainin Derivative
hetero molecules

G: L-ACPC8-Ala-Magainin
H: L-ACPC8-Ala-Magainin

E: L-ACPC8-Ala-Magainin
F: L-ACPC8-Ala-Magainin


Theoretical massNumber of molelcules
Total (without water)20,14310
Polymers20,0728
Non-polymers712
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_757-x+5/2,y+1/2,-z+21
crystal symmetry operation3_758-x+5/2,y+1/2,-z+31
Buried area7630 Å2
ΔGint-94 kcal/mol
Surface area10000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.690, 56.690, 51.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Polypeptide(D)
D-Ala-Magainin Derivative


Mass: 2493.987 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide
L-ACPC8-Ala-Magainin


Mass: 2524.053 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P11006*PLUS
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic pH 5.6 35% v/v tert-butanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→40.09 Å / Num. obs: 8711 / % possible obs: 97.6 % / Redundancy: 12.92 % / Rsym value: 0.111 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 14.61 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2.9 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4MGP

4mgp


Resolution: 2.2→40.09 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.615 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24735 440 5.1 %RANDOM
Rwork0.18187 ---
obs0.18514 8271 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2--0.08 Å20 Å2
3---0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.2→40.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 2 31 1336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191331
X-RAY DIFFRACTIONr_bond_other_d0.0020.021358
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.9331771
X-RAY DIFFRACTIONr_angle_other_deg1.06533085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0955160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.7323.33348
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.70615211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1270.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021464
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02336
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.8864.573692
X-RAY DIFFRACTIONr_mcbond_other4.8784.57691
X-RAY DIFFRACTIONr_mcangle_it6.3396.765852
X-RAY DIFFRACTIONr_mcangle_other6.3366.768853
X-RAY DIFFRACTIONr_scbond_it6.2775.427639
X-RAY DIFFRACTIONr_scbond_other6.2725.431640
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.8767.779920
X-RAY DIFFRACTIONr_long_range_B_refined11.76837.4131501
X-RAY DIFFRACTIONr_long_range_B_other11.77737.3461495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 34 -
Rwork0.162 616 -
obs--100 %

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