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- PDB-7kzl: Cyclopentane peptide nucleic acid in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 7kzl
TitleCyclopentane peptide nucleic acid in complex with DNA
Components
  • DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3')
  • XDJ-XDD-XDY-XDJ-XDY-XDJ-XDD-XDY-XDD-XDV
KeywordsPEPTIDE NUCLEIC ACID/DNA / peptide nucleic acid / PNA / PEPTIDE NUCLEIC ACID-DNA complex
Function / homologyIODIDE ION / METHANOL / DNA
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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: Nucleic Acids Res. / Year: 2021
Title: Conformational constraints of cyclopentane peptide nucleic acids facilitate tunable binding to DNA.
Authors: Zheng, H. / Botos, I. / Clausse, V. / Nikolayevskiy, H. / Rastede, E.E. / Fouz, M.F. / Mazur, S.J. / Appella, D.H.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 3, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / 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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3')
B: XDJ-XDD-XDY-XDJ-XDY-XDJ-XDD-XDY-XDD-XDV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,37313
Polymers5,6962
Non-polymers67811
Water1,74797
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.704, 54.704, 39.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

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DNA chain / Protein/peptide , 2 types, 2 molecules AB

#1: DNA chain DNA (5'-D(*TP*AP*TP*CP*AP*CP*AP*TP*C)-3')


Mass: 2674.787 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein/peptide XDJ-XDD-XDY-XDJ-XDY-XDJ-XDD-XDY-XDD-XDV


Mass: 3021.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 108 molecules

#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MOH / METHANOL


Mass: 32.042 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: CH4O
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 100mM MES, 15% ethanol, 200mM Zinc acetate

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→32.09 Å / Num. obs: 28269 / % possible obs: 99.8 % / Redundancy: 18.4 % / Biso Wilson estimate: 13.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.07 / Net I/σ(I): 35.4
Reflection shellResolution: 1.3→1.34 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 8.2 / Num. unique obs: 2597 / CC1/2: 0.96

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: I-SAD

Resolution: 1.3→32.09 Å / SU ML: 0.0955 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.3569 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1885 1420 5.02 %
Rwork0.1719 26849 -
obs0.1728 28269 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.38 Å2
Refinement stepCycle: LAST / Resolution: 1.3→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 0 411 97 508
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0245443
X-RAY DIFFRACTIONf_angle_d2.3581623
X-RAY DIFFRACTIONf_chiral_restr0.061753
X-RAY DIFFRACTIONf_plane_restr0.019328
X-RAY DIFFRACTIONf_dihedral_angle_d38.5684143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.340.21061640.19962597X-RAY DIFFRACTION98.33
1.34-1.40.23531340.19362733X-RAY DIFFRACTION100
1.4-1.460.22641610.18662660X-RAY DIFFRACTION100
1.46-1.540.20961340.17382699X-RAY DIFFRACTION100
1.54-1.640.18521200.15922722X-RAY DIFFRACTION100
1.64-1.760.15541240.15772710X-RAY DIFFRACTION100
1.76-1.940.19841510.16342687X-RAY DIFFRACTION100
1.94-2.220.19221420.17562700X-RAY DIFFRACTION99.96
2.22-2.80.22851670.17972674X-RAY DIFFRACTION100
2.8-32.090.1531230.16872667X-RAY DIFFRACTION98.27

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