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- PDB-9j3s: De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring... -

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Basic information

Entry
Database: PDB / ID: 9j3s
TitleDe Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure
ComponentsDLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY
KeywordsDE NOVO PROTEIN / CPP / Protein design / Peptide self-assembly / Amphipathic peptides / Cell-penetration
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsPark, J. / Hyun, S. / Lee, S.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: Acs Omega / Year: 2024
Title: De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure
Authors: Park, J. / Hyun, S. / Lee, S.J.
History
DepositionAug 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY
C: DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY
B: DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY
D: DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY
E: DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY
F: DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY


Theoretical massNumber of molelcules
Total (without water)10,8026
Polymers10,8026
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-81 kcal/mol
Surface area6610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.846, 64.846, 106.077
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

#1: Polypeptide(D)
DLE-DLY-DLY-DLE-DCY-DLY-DLE-DLE-DLY-DLY-DLE-DCY-DLY-DLE-DAL-GLY


Mass: 1800.414 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 60% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.26 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.26 Å / Relative weight: 1
ReflectionResolution: 1.6→45.9 Å / Num. obs: 13375 / % possible obs: 99.94 % / Redundancy: 13.6 % / CC1/2: 1 / Net I/σ(I): 24.67
Reflection shellResolution: 1.92→4.39 Å / Num. unique obs: 1304 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→45.85 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 39.74 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3352 651 4.87 %RANDOM
Rwork0.3209 ---
obs0.3216 13375 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.68→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms725 0 0 17 742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009719
X-RAY DIFFRACTIONf_angle_d1.629927
X-RAY DIFFRACTIONf_dihedral_angle_d22.901315
X-RAY DIFFRACTIONf_chiral_restr0.139125
X-RAY DIFFRACTIONf_plane_restr0.00489
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.810.39781190.34522502X-RAY DIFFRACTION100
1.81-1.990.35621400.34362472X-RAY DIFFRACTION100
1.99-2.270.36151400.30022512X-RAY DIFFRACTION100
2.28-2.870.33771160.32242555X-RAY DIFFRACTION100
2.87-45.850.3241360.32112683X-RAY DIFFRACTION100

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