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- PDB-9d2w: [Q:(Cu+):F_pH11] Metal-mediated DNA base pair in a self-assemblin... -

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Basic information

Entry
Database: PDB / ID: 9d2w
Title[Q:(Cu+):F_pH11] Metal-mediated DNA base pair in a self-assembling rhombohedral lattice
Components
  • DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*T)-3')
  • DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
  • DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
  • DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
KeywordsDNA / Tensegrity triangle / mmDNA / thiopurine
Function / homologyCOPPER (II) ION / DNA / DNA (> 10)
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 5.15 Å
AuthorsImstepf, L. / Vecchioni, S. / Sha, R. / Ohayon, Y.P. / Woloszyn, K.
Funding support United States, 3items
OrganizationGrant numberCountry
Office of Naval Research (ONR)N000141912596 United States
National Science Foundation (NSF, United States)CCF-2106790 United States
National Science Foundation (NSF, United States)GCR-2317843 United States
CitationJournal: To Be Published
Title: Thioguanine metal base pairs
Authors: Imstepf, L. / Vecchioni, S.
History
DepositionAug 9, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 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: DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*T)-3')
B: DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')
C: DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')
D: DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9085
Polymers12,8454
Non-polymers641
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-17 kcal/mol
Surface area7400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.939, 105.939, 95.576
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: DNA chain DNA (5'-D(*GP*AP*GP*CP*AP*GP*CP*CP*TP*GP*T)-3')


Mass: 6504.264 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: DNA chain DNA (5'-D(P*CP*CP*AP*(DF)P*AP*CP*A)-3')


Mass: 2082.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*GP*CP*TP*GP*CP*T)-3')


Mass: 2129.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*CP*TP*GP*AP*TP*GP*T)-3')


Mass: 2128.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 8.25 Å3/Da / Density % sol: 85.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM MOPS, 1.25 M magnesium sulfate / Temp details: 338-293 degrees C at 0.4 degrees C/hour

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 23, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 5.15→19.68 Å / Num. obs: 6736 / % possible obs: 83.9 % / Redundancy: 5.6 % / Biso Wilson estimate: 228.5 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.6
Reflection shell
Resolution (Å)Num. unique obsCC1/2Diffraction-ID
5.154-5.9239520.3321
9.794-19.67511250.9981

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
STARANISOdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 5.15→19.68 Å / SU ML: 0.3444 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 23.5933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1994 129 5.41 %
Rwork0.1546 2255 -
obs0.1565 2384 76.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 337.71 Å2
Refinement stepCycle: LAST / Resolution: 5.15→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 860 1 0 861
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053961
X-RAY DIFFRACTIONf_angle_d0.86891476
X-RAY DIFFRACTIONf_chiral_restr0.0428159
X-RAY DIFFRACTIONf_plane_restr0.003542
X-RAY DIFFRACTIONf_dihedral_angle_d36.098435
LS refinement shellResolution: 5.15→19.68 Å
RfactorNum. reflection% reflection
Rfree0.1994 129 -
Rwork0.1546 2255 -
obs--76.51 %

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