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- PDB-7uid: Thyclotides peptide nucleic acid in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7uid
TitleThyclotides peptide nucleic acid in complex with DNA
Components
  • DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')
  • Thyclotide
KeywordsDNA/PEPTIDE NUCLEIC ACID / thyclotides / peptide nucleic acid / PNA / PEPTIDE NUCLEIC ACID-DNA complex / DNA-PEPTIDE NUCLEIC ACID complex
Function / homologyDNA / PEP_NUC
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsBotos, I. / Appella, D.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)ZIA-DK031143 United States
CitationJournal: Jacs Au / Year: 2023
Title: Variation of Tetrahydrofurans in Thyclotides Enhances Oligonucleotide Binding and Cellular Uptake of Peptide Nucleic Acids.
Authors: Zheng, H. / Clausse, V. / Amarasekara, H. / Mazur, S.J. / Botos, I. / Appella, D.H.
History
DepositionMar 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 3.0Jul 2, 2025Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')
C: DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')
B: Thyclotide
D: Thyclotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,11412
Polymers11,6514
Non-polymers4638
Water2,810156
1
A: DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')
B: Thyclotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0576
Polymers5,8262
Non-polymers2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')
D: Thyclotide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0576
Polymers5,8262
Non-polymers2324
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.286, 64.098, 71.244
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222

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Components

#1: DNA chain DNA (5'-D(*GP*AP*TP*GP*TP*GP*AP*TP*A)-3')


Mass: 2794.859 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Peptide nucleic acid Thyclotide


Mass: 3030.674 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 10% PEG 3350, 200mM Zinc Acetate, 100mM Sodium Acetate, pH 4.5

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.54 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 15, 2021 / Details: VariMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→35.62 Å / Num. obs: 8493 / % possible obs: 99.9 % / Redundancy: 12.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.6
Reflection shellResolution: 2→2.05 Å / Rmerge(I) obs: 0.16 / Num. unique obs: 622 / CC1/2: 0.99

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
XDS2021data reduction
XDS2021data scaling
AutoSol1.19phasing
RefinementMethod to determine structure: SAD / Resolution: 2→35.62 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.264 / SU Rfree Blow DPI: 0.197 / SU Rfree Cruickshank DPI: 0.177
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 443 -RANDOM
Rwork0.2321 ---
obs0.2339 8482 97.5 %-
Displacement parametersBiso mean: 22.84 Å2
Baniso -1Baniso -2Baniso -3
1-2.0091 Å20 Å20 Å2
2--0.6524 Å20 Å2
3----2.6615 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2→35.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 372 426 156 954
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121172HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.091922HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d206SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes70HARMONIC5
X-RAY DIFFRACTIONt_it876HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion54SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact903SEMIHARMONIC4
X-RAY DIFFRACTIONt_other_torsion29.65
LS refinement shellResolution: 2→2.03 Å
RfactorNum. reflection% reflection
Rfree0.2457 22 -
Rwork0.2368 --
obs0.2372 386 100 %

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