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

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Basic information

Entry
Database: PDB / ID: 5cgo
TitleStructure of quasiracemic Ala-Magainin 2 with a beta amino acid substitution at position 13
Components
  • ACPC-13 derivative of Ala-Magainin 2
  • D-Ala-Magainin 2
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial / quasiracemate / homochiral dimerization / beta amino acids
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: 1.5 Å
AuthorsHayouka, Z. / Thomas, N.C. / Mortenson, D.E. / Satyshur, K.A. / Weisblum, B. / Forest, K.T. / Gellman, S.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM061238 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: Database references
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 1.4Dec 25, 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 / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACPC-13 derivative of Ala-Magainin 2
B: ACPC-13 derivative of Ala-Magainin 2
C: D-Ala-Magainin 2
D: D-Ala-Magainin 2


Theoretical massNumber of molelcules
Total (without water)10,0364
Polymers10,0364
Non-polymers00
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-34 kcal/mol
Surface area6640 Å2
2
A: ACPC-13 derivative of Ala-Magainin 2
C: D-Ala-Magainin 2
D: D-Ala-Magainin 2

B: ACPC-13 derivative of Ala-Magainin 2


Theoretical massNumber of molelcules
Total (without water)10,0364
Polymers10,0364
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area3270 Å2
ΔGint-40 kcal/mol
Surface area6060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)24.850, 27.000, 29.960
Angle α, β, γ (deg.)109.76, 102.35, 90.23
Int Tables number1
Space group name H-MP1

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Components

#1: Protein/peptide ACPC-13 derivative of Ala-Magainin 2


Mass: 2524.053 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: P11006*PLUS
#2: Polypeptide(D) D-Ala-Magainin 2


Mass: 2493.987 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.78 Å3/Da / Density % sol: 30.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Sodium citrate tribasic dihydrate 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-G / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→27.45 Å / Num. obs: 10964 / % possible obs: 96.1 % / Redundancy: 3.75 % / Rsym value: 0.052 / Net I/σ(I): 14.94
Reflection shellResolution: 1.5→1.6 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.02 / % possible all: 94.4

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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: 1.5→27.45 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.742 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23889 566 5.2 %RANDOM
Rwork0.17166 ---
obs0.17462 10395 96.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.15 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å2-0.54 Å20.02 Å2
2---1.14 Å21.1 Å2
3---1.67 Å2
Refinement stepCycle: LAST / Resolution: 1.5→27.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms690 0 0 45 735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.019721
X-RAY DIFFRACTIONr_bond_other_d0.0020.02769
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.975960
X-RAY DIFFRACTIONr_angle_other_deg1.02531765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.1845.11190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64822.85721
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.90815134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2107
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02789
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02169
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_it1.982.322368
X-RAY DIFFRACTIONr_mcbond_other1.9522.321367
X-RAY DIFFRACTIONr_mcangle_it2.3673.45453
X-RAY DIFFRACTIONr_mcangle_other2.3793.451454
X-RAY DIFFRACTIONr_scbond_it2.5052.787353
X-RAY DIFFRACTIONr_scbond_other2.5082.787352
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7163.949504
X-RAY DIFFRACTIONr_long_range_B_refined4.25319.284796
X-RAY DIFFRACTIONr_long_range_B_other3.31718.824784
X-RAY DIFFRACTIONr_rigid_bond_restr1.20531488
X-RAY DIFFRACTIONr_sphericity_free50.239516
X-RAY DIFFRACTIONr_sphericity_bonded8.82551501
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 41 -
Rwork0.156 731 -
obs--94.96 %

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