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- PDB-9hpp: Helical form of Citropin 1.3 -

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Basic information

Entry
Database: PDB / ID: 9hpp
TitleHelical form of Citropin 1.3
ComponentsCitropin-1.3
KeywordsANTIMICROBIAL PROTEIN / frog / fibril
Function / homologyAurein antibiotic peptide family / Aurein-like antibiotic peptide / defense response to bacterium / extracellular region / Citropin-1.3
Function and homology information
Biological speciesRanoidea citropa (Blue Mountains treefrog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsBloch, Y. / Rayan, B. / Landau, M.
Funding supportEuropean Union, Israel, 2items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission945405European Union
Israel Science Foundation2111/20 Israel
CitationJournal: Adv Sci / Year: 2025
Title: Structural and Functional Versatility of the Amyloidogenic Non-Amidated Variant of the Antimicrobial Peptide Citropin 1.3.
Authors: Strati, F. / Cali, M.P. / Bloch, Y. / Mostafavi, S. / Monistrol, J. / Golubev, A. / Rayan, B. / Gustavsson, E. / Landau, M.
History
DepositionDec 13, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 8, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citropin-1.3
B: Citropin-1.3


Theoretical massNumber of molelcules
Total (without water)3,2642
Polymers3,2642
Non-polymers00
Water1629
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-6 kcal/mol
Surface area2640 Å2
Unit cell
Length a, b, c (Å)67.830, 67.830, 67.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4

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Components

#1: Protein/peptide Citropin-1.3


Mass: 1631.998 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Ranoidea citropa (Blue Mountains treefrog) / References: UniProt: P81846
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.98 Å3/Da / Density % sol: 69.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 2.2
Details: 20%v/v Glycerol, 8%w/v PEG 8,000 and 8%w/v PEG 1,000. Peptide prepared in 2M acetate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.56→47.96 Å / Num. obs: 7919 / % possible obs: 98.1 % / Redundancy: 9.56 % / Biso Wilson estimate: 29.08 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.074 / Net I/σ(I): 14.65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
4.67-47.968.243.353660.9990.0496.1
3.31-4.679.4444.345780.9990.04398.6
1.66-1.779.621.9911760.5831.78399.6
1.56-1.666.720.9511410.332.40790.5

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
REFMAC5.8.043refinement
XDS20230630data reduction
XDS20230630data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→47.96 Å / SU ML: 0.222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.5304
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3233 785 9.99 %
Rwork0.2839 7071 -
obs0.2878 7856 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.41 Å2
Refinement stepCycle: LAST / Resolution: 1.56→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms230 0 0 9 239
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145242
X-RAY DIFFRACTIONf_angle_d1.1527327
X-RAY DIFFRACTIONf_chiral_restr0.065543
X-RAY DIFFRACTIONf_plane_restr0.007239
X-RAY DIFFRACTIONf_dihedral_angle_d17.332291
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.660.38311130.37611016X-RAY DIFFRACTION87.38
1.66-1.790.36271300.29561171X-RAY DIFFRACTION99.69
1.79-1.970.30721310.27861175X-RAY DIFFRACTION100
1.97-2.250.28771300.24341189X-RAY DIFFRACTION99.92
2.25-2.840.26021360.25511216X-RAY DIFFRACTION100
2.84-47.960.351450.29781304X-RAY DIFFRACTION99.18

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